2EXJ | pdb_00002exj

Structure of the family43 beta-Xylosidase D128G mutant from geobacillus stearothermophilus in complex with xylobiose

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.4	285	17% PEG 6000, 0.1M MES, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.383	α = 90
b = 140.383	β = 90
c = 232.907	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2005-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9239	EMBL/DESY, HAMBURG	X12

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	30	99.9			119520	118549

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.23	100

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 (All)	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	2.2	30	119250	118179	5922	99.68	0.208	0.208	0.205	0.21	0.282	0.29	RANDOM	36.489

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]
-0.91			-0.91		1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.084
r_dihedral_angle_4_deg	19.32
r_dihedral_angle_3_deg	17.185
r_dihedral_angle_1_deg	7.256
r_scangle_it	2.539
r_scbond_it	1.717
r_angle_refined_deg	1.616
r_mcangle_it	1.257
r_mcbond_it	0.738
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.084
r_dihedral_angle_4_deg	19.32
r_dihedral_angle_3_deg	17.185
r_dihedral_angle_1_deg	7.256
r_scangle_it	2.539
r_scbond_it	1.717
r_angle_refined_deg	1.616
r_mcangle_it	1.257
r_mcbond_it	0.738
r_nbtor_refined	0.311
r_symmetry_hbond_refined	0.228
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.215
r_metal_ion_refined	0.207
r_xyhbond_nbd_refined	0.201
r_chiral_restr	0.117
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17488
Nucleic Acid Atoms
Solvent Atoms	1651
Heterogen Atoms	140

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.