3QC2 | pdb_00003qc2

Crystal structure of a glycosyl hydrolase (BACOVA_03624) from Bacteroides ovatus at 2.30 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	277	40.0% polyethylene glycol 300, 0.1M phosphate-citrate pH 4.2, Additive: 0.003 M fructose, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.07	α = 90
b = 137.07	β = 90
c = 81.042	γ = 120

Symmetry
Space Group	P 65

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	ADSC QUANTUM 315		2010-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9537,0.9795,0.9793	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.3	28.31	98	0.117	0.145	8.84	5.59		38497		-3	37.479

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.38	89.6		0.705	0.874	1.53

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	2.3	28.31	38468	1931	99.38	0.1864	0.1844	0.18	0.2241	0.22	RANDOM	27.6448

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]
0.74	0.37		0.74		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.542
r_dihedral_angle_3_deg	9.148
r_dihedral_angle_4_deg	9.004
r_dihedral_angle_1_deg	2.938
r_scangle_it	1.33
r_angle_refined_deg	1.234
r_scbond_it	0.851
r_angle_other_deg	0.798
r_mcangle_it	0.621
r_mcbond_it	0.326

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.542
r_dihedral_angle_3_deg	9.148
r_dihedral_angle_4_deg	9.004
r_dihedral_angle_1_deg	2.938
r_scangle_it	1.33
r_angle_refined_deg	1.234
r_scbond_it	0.851
r_angle_other_deg	0.798
r_mcangle_it	0.621
r_mcbond_it	0.326
r_chiral_restr	0.074
r_mcbond_other	0.051
r_bond_refined_d	0.015
r_gen_planes_refined	0.004
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5662
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	47

Software

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