4E9K | pdb_00004e9k

Crystal structure of a DUF4465 family protein (BACOVA_04221) from Bacteroides ovatus ATCC 8483 at 2.31 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	2.4M ammonium sulfate, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.07	69.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.156	α = 90
b = 93.156	β = 90
c = 103.109	γ = 90

Symmetry
Space Group	P 41 2 2

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 PILATUS 6M	Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)	2012-02-09	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837,0.97975,0.97908	SSRL	BL11-1

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	2.31	45.108	99.8	0.085	16.38			20538		-3	50.557

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	2.31	2.39	99.9		0.875	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	2.31	45.108	20507	1041	99.81	0.1798	0.1785	0.19	0.2038	0.21	RANDOM	55.8103

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]
1.2			1.2		-2.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.047
r_dihedral_angle_4_deg	18.213
r_dihedral_angle_3_deg	13.826
r_dihedral_angle_1_deg	7.599
r_angle_refined_deg	1.606
r_angle_other_deg	0.861
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.047
r_dihedral_angle_4_deg	18.213
r_dihedral_angle_3_deg	13.826
r_dihedral_angle_1_deg	7.599
r_angle_refined_deg	1.606
r_angle_other_deg	0.861
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1917
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	20

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.