4HZ7

Crystal structure of BglB with glucose


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 295.0
Details 0.1M Tris, pH 7.0-7.4, 0.8M Na/K tartaric acid, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.38 α = 90
b = 71.34 β = 90
c = 86.98 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2008-11-14
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.23 PAL/PLS 6C1

Data Collection

Overall
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
2 20 95.8 -- -- -- -- 28542 28542 2.0 2.0 --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.0 2.07 95.8 -- -- -- -- --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.0 19.95 -- 0.0 -- 28517 2827 94.46 0.1479 0.1479 0.1419 0.2024 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.001 2.053 -- 151 1382 0.2 0.271 -- 70.52
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.1087
Anisotropic B[1][1] -0.9
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.96
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 22.7
r_bond_refined_d 0.021
r_sphericity_free 7.907
r_scbond_it 3.747
r_scangle_it 5.721
r_dihedral_angle_2_deg 36.188
r_angle_refined_deg 1.621
r_chiral_restr 0.115
r_gen_planes_refined 0.008
r_mcbond_it 1.497
r_mcangle_it 2.535
r_rigid_bond_restr 2.453
r_dihedral_angle_3_deg 13.983
r_sphericity_bonded 2.987
r_dihedral_angle_1_deg 5.282
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3531
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 277

Software

Software
Software Name Purpose
REFMAC refinement version: 5.5.0110
PDB_EXTRACT data extraction version: 3.11
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing