5DT7 | pdb_00005dt7

Crystal structure of the GH1 beta-glucosidase from Exiguobacterium antarcticum B7 in space group C2221

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 CAPS (pH 10.5), 0.2 M lithium sulfate and 2 M ammonium sulfate using in situ proteolysis (1:1000 (w/w) ratio of trypsin:protein

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.975	α = 90
b = 376.119	β = 90
c = 109.487	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	PIXEL	DECTRIS PILATUS 2M		2014-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE W01B-MX2	1.459	LNLS	W01B-MX2

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	2.15	50	99	0.086	0.103	8.19	3.1		123301		-3	42.751

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	2.15	2.28	96		0.756	0.965	1.17

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	2.15	20	123301	6550	99.52	0.189	0.1875	0.2	0.2175	0.23	RANDOM	44.182

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]
-0.79			-0.62		1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_4_deg	18.044
r_dihedral_angle_3_deg	12.921
r_dihedral_angle_1_deg	6.562
r_mcangle_it	2.34
r_mcbond_it	1.545
r_mcbond_other	1.545
r_angle_refined_deg	1.36
r_angle_other_deg	0.955
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.302
r_dihedral_angle_4_deg	18.044
r_dihedral_angle_3_deg	12.921
r_dihedral_angle_1_deg	6.562
r_mcangle_it	2.34
r_mcbond_it	1.545
r_mcbond_other	1.545
r_angle_refined_deg	1.36
r_angle_other_deg	0.955
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14456
Nucleic Acid Atoms
Solvent Atoms	519
Heterogen Atoms	121

Software

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