4QHB | pdb_00004qhb

Crystal structure of a putative hydrolase (BVU_2763) from Bacteroides vulgatus ATCC 8482 at 2.44 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.050M lithium sulfate, 10.00% Glycerol, 30.00% polyethylene glycol 600, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.102	α = 90
b = 107.296	β = 101.82
c = 108.137	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2014-02-26	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.96109,0.97934,0.97911	SSRL	BL14-1

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	2.44	47.852	99.8	0.118	8.79			69089		-3	40.515

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	2.44	2.53	99.7		0.605	2.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.44	47.852	69063	3499	99.79	0.1723	0.17	0.18	0.215	0.22	RANDOM	36.9303

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]
-1.21		-1.1	2.48		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.722
r_dihedral_angle_4_deg	16.234
r_dihedral_angle_3_deg	11.582
r_dihedral_angle_1_deg	4.096
r_angle_refined_deg	1.625
r_angle_other_deg	1.132
r_chiral_restr	0.059
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.722
r_dihedral_angle_4_deg	16.234
r_dihedral_angle_3_deg	11.582
r_dihedral_angle_1_deg	4.096
r_angle_refined_deg	1.625
r_angle_other_deg	1.132
r_chiral_restr	0.059
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12260
Nucleic Acid Atoms
Solvent Atoms	638
Heterogen Atoms	88

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
XDS	data reduction
SHELXD	phasing

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.