6GJT

Chlamydia protein Pgp3 studied at high resolution in a new crystal form

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	A 7mg per ml Pgp3 stock buffered with 220mM NaCl, 50mM Tris-HCl pH 7.5 and 5mM DTT was screened for suitable crystallization conditions in sitting drop vapour diffusion format using a Mosquito robot (TTP Labtech, UK). A variety of commercially available screens such as Crystal Screen HT, Index HT (Hampton Research, USA), Morpheus and PGA (Molecular Dimensions, UK) were used in 96 well MRC crystallization plates (Molecular Dimensions, UK). All screening trials contained 400 nanolitre drops, each mixed in a 1 to 1 ratio of the protein and the screen solutions. The crystallization trials were incubated at 293K. The different leads obtained from the crystallization screening trials were optimised by determining working phase diagrams as detailed in Saridakis and Chayen (Saridakis & Chayen 2000). Each optimisation trial was also scaled up to 1 microlitre drop volume and set up manually in hanging drops (Qiagen Nextal plates) and in microbatch experiments (Chayen 1999).

Crystal Properties
Matthews coefficient	Solvent content
2.68	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.41	α = 90
b = 108.25	β = 90
c = 207	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 S 6M		2012-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9173	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.98	45.7	98.1	0.2	9.7	11.7		130981			26.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.98	2	98.3		1.875	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4JDM	1.98	42.62	124208	6594	97.77	0.27407	0.2731	0.2922	RANDOM	36.304

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.01			-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.866
r_dihedral_angle_4_deg	17.051
r_dihedral_angle_3_deg	15.091
r_long_range_B_refined	8.798
r_long_range_B_other	8.798
r_dihedral_angle_1_deg	6.764
r_scangle_other	6.227
r_mcangle_other	5.132
r_mcangle_it	5.13
r_scbond_it	4.29
r_scbond_other	4.289
r_mcbond_it	3.68
r_mcbond_other	3.674
r_angle_refined_deg	1.838
r_angle_other_deg	1.683
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.013
r_bond_other_d	0.011
r_gen_planes_other	0.009
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7950
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing