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RE: [ccp4bb]: spacegroup problem



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Dear Sameeta,
 
we have a troublesome case that sound a lot like yours. We have exactly the same behaviour for crytals obtained for a protein complex, diffracting to 1.8 A. We can either index in P4122 or I4122 depending on how you play around with the programs and how long you expose your crystals for (all P4 specific reflections are very weak). We could solve the structure using MIR (both in P4122 and I4122) leading to great maps, but we could only build 1 out of the 2 proteins.....and that structure refines to approx 27% R 31% Rfree...... Turns out that partner 1 makes up the entire lattice with partner 2 only binding to partner 1 without contributing to the lattice. However, partner 1 is a tetramer that has 1 monomer in the AU, the monomeric partner 2 binds to 2 (!) monomers of partner 1. This results in partner 2 occupying throughout the cell two different, but mutually exclusive positions. You could look at it as if the AU has 2 copies of  partner 2 each at approx 50% occupancy and bo!
 th overlapping, making the density not very interpretable to say the least. By carefull analysis of anomalous data we could actually confirm the position of a heavy atom native to the partner 2 structure. Using reliable models available for partner 2 and the position of the heavy atom it turns out we seem to be right: applying either P4 or I4 symmetry makes all partner 2 models superimpose. I think this explains perhaps the very weak P4 reflections, as on a very microscopic scale the crystal is obviously heterogenous, having partner 2 in either position A or B for all unit cells resulting in the odd and diffuse reflections seen in between the strong and sharp I4122 reflections. Overall, the crystal diffracts like it is I4122. Explaining this particular case has always been difficult without graphics to illustrate it, but i hope this makes sense.
 
Needless to say we have returned to find other crystallisation conditions. I would be very interested to find out if anyone else has ever encountered similar case(s), and even more if they have found a solution to this kind of problem.
 
yours,
 
David Leys
 
Crystallography Group,
University Of Leicester
www.le.ac.uk/biochem/pcem1/Xraywebsite/leys.htm
 
 
 
 
 
Original Message----- 
From: sameeta bilgrami [mailto:sameeta_b@yahoo.co.in] 
Sent: Fri 28/03/2003 15:33 
To: ccp4bb@dl.ac.uk 
Cc: 
Subject: [ccp4bb]: spacegroup problem



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	***          CCP4 home page http://www.ccp4.ac.uk         ***
	
	dear all,
	     hello,
	        I have asked this question once before, but i
	think now i have more data and information and
	threfore can present my problem in a better way.
	        I have a set of datasets collected at
	synchroton.( native till 1.9 a resolution and four
	derivatives till 2.2 A resolution, Hgcl2 HgCN, Pt and
	Pb). There is an ambiguity in spacegroup for these
	crystals. Denzo gives P tetragonal if allowed to take
	the default no. of spots. It gives I tetragonal if the
	no. of spots taken for autoindexing are reduced. Same
	is the case with automar. Somebody suggested that i
	should take two images 90 degrees apart and see. Two
	images taken 90 degree apart does reduce the error ,
	but the trick remains the same less no. of spots give
	I tetragonal and more no. of spots give P tetragonal.
	I then tried mosflm. Here i do not know how to change
	the no. of spots to be taken and so I treid with
	default no. of spots. It gave varying results. It gave
	P tetragonal for the native and the Pt. crytal but
	gave I tetragonal for the rest of the derivatives.
	     I have also calculated native patterson till 2.2
	a resolution with the P tetragonal mtz file for all
	datasets. All the datasets give very large off origin
	peak at 1/2, 1/2, 1/2. The origin peak is on an
	average ~110 and the one at 1/2, 1/2, 1/2 is about 88.
	      I looked at h+k+l=2n+1 reflections in the sca
	file of P tetragonal. Many reflections are weak but
	many are present.
	       I have an earlier set of datasets( 1 native
	till 2.5 and 3 derivatives also till 2.5) collected in
	house. These crystals unambiguosly give the spacegroup
	as I tetragonal. The cell parameters of both the
	datasets (collected in house and those at synchroton)
	are the same.
	        From the data collected in house i could
	manage to build a partial model ( a little less than
	half of the structure). The heavy atom derivatives
	were not  very  good and that is why i had tried to
	collect another datset at the synchroton. My protein
	does not have much regular secondary structure and the
	phases also not being good i was not sure wether i had
	traced the right path or not. So i used this model for
	MR with the native data collected in house and i got a
	good enough solution. Emboldened i tried my hand at
	the native collected at synchroton. This did not give
	the solution in P43212/p41212(as suggested by
	sytamatic absences) Neither did it give solution in
	any of the other P tetragonal spacegroups. I then
	tried the mtz file of I4122 and I did get a solution.
	      What does this suggest? does this mean that my
	real space group is  I tetragonal
	
	An off origin peak at 1/2 1/2 1/2 may suggest
	pseudotranslational symmetry....but ..what if i
	process an I tetrgonal as Ptetragonal wont that also
	give a peak at 1/2, 1/2, 1/2. How do we distinguish
	between these two cases.....
	
	there are certainly certain changes taking place at
	the synchroton that make the data collected there to
	have an ambiguity with regards to the spacegroups
	though the same crystals give umambiguous spacegroup
	with data collected in house.  What implication these
	changes have with regards to the isomorphism of a set
	of datasets collected at synchroton. This is because
	the same sort of "change" may not occur for different
	crystals. I am sayiing this because though i am
	observing large differences between the native and
	derivatives, i am ending up with bad phasing
	statistics with solve and mlphare ( i have tried
	p43212, p41212 and i4122)
	 What else can i do to build up more of my model
	(apart from trying to collect another better set of
	derivatives)
	         Thankyou all for your kind attention.  Thanks
	in advance for all the suggestions.
	                  Yours sincerely,
	                      Sameeta Bilgrami
	
	
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	-----Original Message----- 
	From: sameeta bilgrami [mailto:sameeta_b@yahoo.co.in] 
	Sent: Fri 28/03/2003 15:33 
	To: ccp4bb@dl.ac.uk 
	Cc: 
	Subject: [ccp4bb]: spacegroup problem
	
	

	***  For details on how to be removed from this list visit the  ***
	***          CCP4 home page http://www.ccp4.ac.uk         ***
	
	dear all,
	     hello,
	        I have asked this question once before, but i
	think now i have more data and information and
	threfore can present my problem in a better way.
	        I have a set of datasets collected at
	synchroton.( native till 1.9 a resolution and four
	derivatives till 2.2 A resolution, Hgcl2 HgCN, Pt and
	Pb). There is an ambiguity in spacegroup for these
	crystals. Denzo gives P tetragonal if allowed to take
	the default no. of spots. It gives I tetragonal if the
	no. of spots taken for autoindexing are reduced. Same
	is the case with automar. Somebody suggested that i
	should take two images 90 degrees apart and see. Two
	images taken 90 degree apart does reduce the error ,
	but the trick remains the same less no. of spots give
	I tetragonal and more no. of spots give P tetragonal.
	I then tried mosflm. Here i do not know how to change
	the no. of spots to be taken and so I treid with
	default no. of spots. It gave varying results. It gave
	P tetragonal for the native and the Pt. crytal but
	gave I tetragonal for the rest of the derivatives.
	     I have also calculated native patterson till 2.2
	a resolution with the P tetragonal mtz file for all
	datasets. All the datasets give very large off origin
	peak at 1/2, 1/2, 1/2. The origin peak is on an
	average ~110 and the one at 1/2, 1/2, 1/2 is about 88.
	      I looked at h+k+l=2n+1 reflections in the sca
	file of P tetragonal. Many reflections are weak but
	many are present.
	       I have an earlier set of datasets( 1 native
	till 2.5 and 3 derivatives also till 2.5) collected in
	house. These crystals unambiguosly give the spacegroup
	as I tetragonal. The cell parameters of both the
	datasets (collected in house and those at synchroton)
	are the same.
	        From the data collected in house i could
	manage to build a partial model ( a little less than
	half of the structure). The heavy atom derivatives
	were not  very  good and that is why i had tried to
	collect another datset at the synchroton. My protein
	does not have much regular secondary structure and the
	phases also not being good i was not sure wether i had
	traced the right path or not. So i used this model for
	MR with the native data collected in house and i got a
	good enough solution. Emboldened i tried my hand at
	the native collected at synchroton. This did not give
	the solution in P43212/p41212(as suggested by
	sytamatic absences) Neither did it give solution in
	any of the other P tetragonal spacegroups. I then
	tried the mtz file of I4122 and I did get a solution.
	      What does this suggest? does this mean that my
	real space group is  I tetragonal
	
	An off origin peak at 1/2 1/2 1/2 may suggest
	pseudotranslational symmetry....but ..what if i
	process an I tetrgonal as Ptetragonal wont that also
	give a peak at 1/2, 1/2, 1/2. How do we distinguish
	between these two cases.....
	
	there are certainly certain changes taking place at
	the synchroton that make the data collected there to
	have an ambiguity with regards to the spacegroups
	though the same crystals give umambiguous spacegroup
	with data collected in house.  What implication these
	changes have with regards to the isomorphism of a set
	of datasets collected at synchroton. This is because
	the same sort of "change" may not occur for different
	crystals. I am sayiing this because though i am
	observing large differences between the native and
	derivatives, i am ending up with bad phasing
	statistics with solve and mlphare ( i have tried
	p43212, p41212 and i4122)
	 What else can i do to build up more of my model
	(apart from trying to collect another better set of
	derivatives)
	         Thankyou all for your kind attention.  Thanks
	in advance for all the suggestions.
	                  Yours sincerely,
	                      Sameeta Bilgrami
	
	
	________________________________________________________________________
	Missed your favourite TV serial last night? Try the new, Yahoo! TV.
	       visit http://in.tv.yahoo.com