3VZJ
Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1HV1 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 298 | 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.02 | 39.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 52.174 | α = 90 |
b = 86.737 | β = 89.89 |
c = 73.09 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | IMAGE PLATE | MAR scanner 345 mm plate | 2008-06-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.541 |
Data Collection
Overall | |||||||||||||||||||
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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 | 2.4 | 38.167 | 91 | 35327 | 31471 | 1 | 1 | 34 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | 1HV1 | 2.406 | 38.167 | 1.41 | 17143 | 16311 | 832 | 64.35 | 0.24 | 0.2442 | 0.2388 | 0.3434 | RANDOM | 30.8582 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-1.1806 | -0.0108 | -0.761 | 1.9416 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 20.684 |
f_angle_d | 1.237 |
f_chiral_restr | 0.085 |
f_bond_d | 0.008 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5796 |
Nucleic Acid Atoms | |
Solvent Atoms | 74 |
Heterogen Atoms | 10 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
SCALA | data scaling |