3GM8 | pdb_00003gm8

Crystal structure of a beta-glycosidase from Bacteroides vulgatus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	294	100mM Tris HCl pH 8.0, 28% PEG 3350, 150mM ammonium sulfate, vapor diffusion, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.754	α = 90
b = 193.348	β = 90
c = 190.667	γ = 90

Symmetry
Space Group	C 2 2 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	MAR CCD 165 mm		2009-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	43.769	98.3	0.144	0.144	8.4	5	45796	45017			43

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	2.4	2.53	99.2		0.465	0.465	2.9	5	6555

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.4	20	45779	44941	2277	98.17	0.229	0.226	0.23	0.287	0.29	RANDOM	51.116

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]
0.58			0.72		-1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.894
r_dihedral_angle_4_deg	19.946
r_dihedral_angle_3_deg	15.209
r_dihedral_angle_1_deg	6.899
r_scangle_it	3.133
r_scbond_it	2.027
r_angle_refined_deg	1.572
r_mcangle_it	1.368
r_angle_other_deg	0.909
r_mcbond_it	0.721
r_mcbond_other	0.142
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6112
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	12

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building