4ZGF | pdb_00004zgf

Crystal structure of a duf4847 family protein (BVU_2626) from Bacteroides vulgatus ATCC 8482 at 1.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1M HEPES pH 7.5, 40% polyethylene glycol 400, 0.2M calcium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.747	α = 90
b = 55.486	β = 90
c = 76.176	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	CCD	MARMOSAIC 325 mm CCD	Vertical focusing mirror; double crystal Si(111) monochromator	2015-02-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.95369,0.97946,0.9793	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	29.304	98.2	0.038	0.05	12.26	2.035		72996		-3	6.458

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1	1.04	93.4		0.644	0.851	1.4

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	1	29.304	72915	3681	99.41	0.117	0.116	0.12	0.1365	0.14	RANDOM	12.2306

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]
-0.15			-0.05		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.31
r_sphericity_free	25.909
r_dihedral_angle_4_deg	10.384
r_dihedral_angle_3_deg	10.315
r_sphericity_bonded	7.062
r_dihedral_angle_1_deg	6.208
r_rigid_bond_restr	2.399
r_angle_refined_deg	1.721
r_angle_other_deg	1.01
r_mcangle_it	0.892

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.31
r_sphericity_free	25.909
r_dihedral_angle_4_deg	10.384
r_dihedral_angle_3_deg	10.315
r_sphericity_bonded	7.062
r_dihedral_angle_1_deg	6.208
r_rigid_bond_restr	2.399
r_angle_refined_deg	1.721
r_angle_other_deg	1.01
r_mcangle_it	0.892
r_mcbond_it	0.684
r_mcbond_other	0.676
r_chiral_restr	0.115
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1114
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	84

Software

Software
Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
REFMAC	refinement
SHELXD	phasing
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.