3OTN | pdb_00003otn

Crystal structure of a SusD superfamily protein (BDI_3964) from Parabacteroides distasonis ATCC 8503 at 1.95 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	0.17M sodium acetate, 25.3% polyethylene glycol 4000, 15.0% Glycerol, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.74	α = 90
b = 92.479	β = 90
c = 152.104	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		2010-07-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97918,0.97896	SSRL	BL9-2

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	1.95	29.37	99.2	0.123	7.7	3.8	76628	76628			20.344

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	1.95	2	100		0.699	0.699	2	3.7	5660

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	1.95	29.37	76591	3860	98.82	0.146	0.1436	0.15	0.1906	0.2	RANDOM	27.8721

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]
0.71			-0.68		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.73
r_dihedral_angle_4_deg	18.006
r_dihedral_angle_3_deg	11.968
r_scangle_it	6.1
r_dihedral_angle_1_deg	5.32
r_scbond_it	4.553
r_mcangle_it	2.808
r_mcbond_it	1.8
r_angle_refined_deg	1.451
r_angle_other_deg	1.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.73
r_dihedral_angle_4_deg	18.006
r_dihedral_angle_3_deg	11.968
r_scangle_it	6.1
r_dihedral_angle_1_deg	5.32
r_scbond_it	4.553
r_mcangle_it	2.808
r_mcbond_it	1.8
r_angle_refined_deg	1.451
r_angle_other_deg	1.088
r_mcbond_other	0.522
r_chiral_restr	0.093
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7591
Nucleic Acid Atoms
Solvent Atoms	847
Heterogen Atoms	148

Software

Software
Software Name	Purpose
SOLVE	phasing
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
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.