3U22 | pdb_00003u22

Crystal structure of a putative HmuY_like heme binding protein (BVU_2192) from Bacteroides vulgatus ATCC 8482 at 2.12 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M bicine pH 9, 1.6M ammonium sulfate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.415	α = 90
b = 128.415	β = 90
c = 110.785	γ = 120

Symmetry
Space Group	P 31 2 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	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)	2011-07-20	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97922,0.97889	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.12	78.487	100	0.118	9.6	5.7	60126	60126

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.23	100		0.01	1.019	0.7	5.8	8674

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	2.12	78.487	60066	3029	99.87	0.1651	0.1647	0.17	0.1724	0.18	RANDOM	48.5786

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]
1.9	0.95		1.9		-2.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.671
r_dihedral_angle_4_deg	14.484
r_dihedral_angle_3_deg	11.171
r_dihedral_angle_1_deg	4.408
r_angle_refined_deg	1.822
r_angle_other_deg	1.343
r_chiral_restr	0.111
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.671
r_dihedral_angle_4_deg	14.484
r_dihedral_angle_3_deg	11.171
r_dihedral_angle_1_deg	4.408
r_angle_refined_deg	1.822
r_angle_other_deg	1.343
r_chiral_restr	0.111
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2893
Nucleic Acid Atoms
Solvent Atoms	275
Heterogen Atoms	104

Software

Software
Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
SCALA	data scaling
REFMAC	refinement
MOSFLM	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.