4R03 | pdb_00004r03

Crystal structure of a DUF3836 family protein (BDI_3222) from Parabacteroides distasonis ATCC 8503 at 1.50 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	277	40.00% 2-methyl-2,4-pentanediol, 0.1M phosphate-citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.001	α = 90
b = 71.697	β = 90
c = 82.683	γ = 90

Symmetry
Space Group	I 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	2014-06-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.95369,0.97934,0.97907	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	1.5	27.084	98.2	0.045	14.96			27948		-3	18.114

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	1.5	1.6	91.2		0.483	1.9

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	1.5	27.084	26540	1407	98.15	0.1675	0.1664	0.17	0.1876	0.2	RANDOM	22.887

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]
0.14			0.25		-0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.862
r_dihedral_angle_3_deg	11.53
r_dihedral_angle_4_deg	9.996
r_dihedral_angle_1_deg	6.173
r_mcangle_it	3.077
r_mcbond_it	1.924
r_mcbond_other	1.912
r_angle_refined_deg	1.736
r_angle_other_deg	0.784
r_chiral_restr	0.115

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.862
r_dihedral_angle_3_deg	11.53
r_dihedral_angle_4_deg	9.996
r_dihedral_angle_1_deg	6.173
r_mcangle_it	3.077
r_mcbond_it	1.924
r_mcbond_other	1.912
r_angle_refined_deg	1.736
r_angle_other_deg	0.784
r_chiral_restr	0.115
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	925
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	31

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.