4K61 | pdb_00004k61

Crystal structure of a DUF2874 family protein (BACUNI_01296) from Bacteroides uniformis ATCC 8492 at 1.70 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.05M calcium acetate, 40% 1,2-propanediol, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.773	α = 90
b = 86.773	β = 90
c = 85.633	γ = 90

Symmetry
Space Group	I 4

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)	2013-03-21	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97926,0.91837	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	1.7	27.44	97.6	0.046	13.29			34782		-3	25.537

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	1.7	1.76	93.2		0.788	1.5

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	1.7	27.44	34780	1745	99.7	0.1909	0.1897	0.2	0.212	0.22	RANDOM	37.9645

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]
1.55			1.55		-3.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.971
r_dihedral_angle_3_deg	14.433
r_dihedral_angle_4_deg	11.117
r_dihedral_angle_1_deg	6.375
r_mcangle_it	3.889
r_mcbond_it	2.393
r_mcbond_other	2.393
r_angle_refined_deg	1.392
r_angle_other_deg	1.012
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.971
r_dihedral_angle_3_deg	14.433
r_dihedral_angle_4_deg	11.117
r_dihedral_angle_1_deg	6.375
r_mcangle_it	3.889
r_mcbond_it	2.393
r_mcbond_other	2.393
r_angle_refined_deg	1.392
r_angle_other_deg	1.012
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2220
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms

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.