4Q69 | pdb_00004q69

Crystal structure of a SusD homolog (BT2259) from Bacteroides thetaiotaomicron VPI-5482 at 2.50 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.1M sodium citrate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.49	64.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.124	α = 90
b = 135.124	β = 90
c = 139.567	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	double crystal monochromator	2014-02-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.95369,0.97936,0.97918	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	2.5	89.672	100	0.155	9	6.2	51369	51369

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	2.5	2.56	100		0.01	1.01	1.9	6.3	3759

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	2.5	89.672	51309	2605	99.83	0.1733	0.172	0.18	0.1989	0.21	RANDOM	45.4606

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]
0.42	0.42		0.42		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.84
r_dihedral_angle_4_deg	16.848
r_dihedral_angle_3_deg	14.221
r_dihedral_angle_1_deg	4.745
r_mcangle_it	4.011
r_mcbond_other	2.589
r_mcbond_it	2.588
r_angle_refined_deg	0.998
r_angle_other_deg	0.778
r_chiral_restr	0.057

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.84
r_dihedral_angle_4_deg	16.848
r_dihedral_angle_3_deg	14.221
r_dihedral_angle_1_deg	4.745
r_mcangle_it	4.011
r_mcbond_other	2.589
r_mcbond_it	2.588
r_angle_refined_deg	0.998
r_angle_other_deg	0.778
r_chiral_restr	0.057
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7188
Nucleic Acid Atoms
Solvent Atoms	292
Heterogen Atoms	9

Software

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