3VZN
Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) N35E mutant with Glu78 covalently bonded to 2-deoxy-2-fluoro-xylobiose
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1BVV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 298 | 13-20% (NH4)2SO4, 40mM Tris-HCl, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.89 | 34.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.395 | α = 90 |
b = 63.038 | β = 104.89 |
c = 64.36 | 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 | 2008-07-01 | 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 | 1.67 | 60 | 98.1 | 51981 | 49715 | 1 | 1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1BVV | 1.67 | 44.28 | 34541 | 32247 | 1722 | 95.89 | 0.19083 | 0.18845 | 0.23562 | RANDOM | 24.222 |
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] | |
-0.52 | -1.33 | -0.44 | 0.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.329 |
r_dihedral_angle_4_deg | 15.046 |
r_dihedral_angle_3_deg | 12.461 |
r_dihedral_angle_1_deg | 8.778 |
r_scangle_it | 3.799 |
r_scbond_it | 2.883 |
r_angle_refined_deg | 1.929 |
r_mcangle_it | 1.874 |
r_mcbond_it | 1.165 |
r_chiral_restr | 0.157 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2898 |
Nucleic Acid Atoms | |
Solvent Atoms | 230 |
Heterogen Atoms | 51 |
Software
Software | |
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Software Name | Purpose |
MAR345dtb | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |