7VXR | pdb_00007vxr

Crystal structure of BPSL1038 from Burkholderia pseudomallei

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7VXT	7VXT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.1 M sodium acetate pH 4.6, 1.8-2M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.36	α = 90
b = 115.63	β = 90
c = 46.73	γ = 90

Symmetry
Space Group	C 2 2 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		2013-12-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.55	28.08	99.1	0.084	0.09	0.031	0.996	12.3	7.7		33712			15.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	89.8		0.563	0.616	0.24	0.896	2.9	5.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7VXT	1.55	28.08	31997	1697	99.1	0.1202	0.1182	0.1184	0.1569	0.1568	RANDOM	28.224

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]
0.52			-1.32		0.8

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	53.612
r_dihedral_angle_2_deg	40.462
r_sphericity_bonded	21.712
r_dihedral_angle_3_deg	14.215
r_dihedral_angle_4_deg	8.241
r_dihedral_angle_1_deg	6.028
r_rigid_bond_restr	5.602
r_angle_refined_deg	2.051
r_angle_other_deg	1.359
r_chiral_restr	0.142
r_bond_refined_d	0.022
r_gen_planes_refined	0.011
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1472
Nucleic Acid Atoms
Solvent Atoms	161
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing