4GGQ | pdb_00004ggq

Crystal structure of a SMT fusion Peptidyl-prolyl cis-trans isomerase from Burkholderia pseudomallei complexed with CJ40

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Internal tracking number 235051a1. Puck IBH5-4, Morpheus well A1. 10% PEG 20,000, 20% PEG MME550, 0.03M Divalent Catios (MgCl2, CaCl2), 0.1M MES/Imidazole pH 6.5, Direct Cryo. BupsA.00130.a.D21, 20.00 mg/ml, CJ40 (EBSI2855), vapor diffusion, sitting drop, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.44	α = 95.07
b = 76.15	β = 90.13
c = 76.35	γ = 92.65

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2012-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.976484	ALS	5.0.3

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	1.95	38.02	97	0.053	12.61	2.4	56274	54575		-3	34.152

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	1.95	2	95.8		0.507	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR	THROUGHOUT	1.95	38.02	56274	54575	2786	96.99	0.189	0.189	0.187	0.19	0.22	0.22	RANDOM	33.607

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]
0.82	0.16	0.03	-0.12	-0.12	-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.941
r_dihedral_angle_3_deg	12.434
r_dihedral_angle_4_deg	10.868
r_dihedral_angle_1_deg	6.398
r_angle_refined_deg	1.475
r_angle_other_deg	1.241
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.941
r_dihedral_angle_3_deg	12.434
r_dihedral_angle_4_deg	10.868
r_dihedral_angle_1_deg	6.398
r_angle_refined_deg	1.475
r_angle_other_deg	1.241
r_chiral_restr	0.09
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.007
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5398
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	145

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
BOS	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.