3B8S
Crystal structure of wild-type chitinase A from Vibrio harveyi
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3B9E | PDB ENTRY 3B9E |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8 | 288 | 1.20M Ammonium Sulfate, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.3 | 46.9 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.267 | α = 91.74 |
b = 64.283 | β = 91.18 |
c = 83.522 | γ = 112.91 |
Symmetry | |
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Space Group | P 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 | RIGAKU RAXIS IV++ | 2006-01-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | 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 | |||||||
1 | 2 | 24.62 | 94.6 | 0.066 | 0.076 | 19.5 | 4 | 73693 | 73693 | 19.5 | 17.7 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
2 | 2.11 | 91.9 | 0.228 | 0.263 | 5.5 | 4 | 10404 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 3B9E | 2 | 24.62 | 73693 | 69969 | 3724 | 94.61 | 0.17022 | 0.17022 | 0.16836 | 0.2051 | RANDOM | 16.188 |
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] | |
0.37 | -0.71 | 0.3 | -0.97 | -0.21 | 0.04 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.885 |
r_dihedral_angle_3_deg | 12.437 |
r_dihedral_angle_4_deg | 10.338 |
r_dihedral_angle_1_deg | 5.165 |
r_scangle_it | 1.421 |
r_angle_refined_deg | 0.968 |
r_scbond_it | 0.946 |
r_mcangle_it | 0.597 |
r_mcbond_it | 0.453 |
r_nbtor_refined | 0.301 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8708 |
Nucleic Acid Atoms | |
Solvent Atoms | 1091 |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrystalClear | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |