5DT5 | pdb_00005dt5

Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group P21

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4PTV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	0.1 M TRIS (pH 8.5), 2% (v/v) PEG400 and 1.45 M lithium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.073	α = 90
b = 104.599	β = 105.8
c = 199.186	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2015-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.24	49.11	97.4	0.103	9.54	3.9		203452

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	4PTV	2.24	49.11	190890	9851	96.04	0.2103	0.2094	0.21	0.2287	0.23	RANDOM	44.132

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]
13.02		13.94	-1.45		-11.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	12.967
r_dihedral_angle_1_deg	6.091
r_mcangle_it	1.436
r_angle_refined_deg	1.103
r_angle_other_deg	0.889
r_mcbond_it	0.818
r_mcbond_other	0.818
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.145
r_dihedral_angle_4_deg	16.766
r_dihedral_angle_3_deg	12.967
r_dihedral_angle_1_deg	6.091
r_mcangle_it	1.436
r_angle_refined_deg	1.103
r_angle_other_deg	0.889
r_mcbond_it	0.818
r_mcbond_other	0.818
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_bond_other_d	0.006
r_gen_planes_refined	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28766
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	25

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

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.