4Z6S
Structure of H200Q variant of Homoprotocatechuate 2,3-Dioxygenase from B.fuscum in complex with 4-sulfonyl catechol at 1.42 Ang resolution
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3OJT |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 13% PEG6000, 0.1M calcium chloride, 0.1M Tris-HCl |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.43 | 49.35 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 110.568 | ¦Á = 90 |
b = 151.99 | ¦Â = 90 |
c = 96.356 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 2 |
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 | CCD | MARMOSAIC 225 mm CCD | 2008-11-14 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | 1.000 | SLS | X06DA |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.42 | 47.952 | 98.4 | 0.073 | 0.082 | 0.038 | 11.8 | 4.5 | 299060 | 299060 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.42 | 1.5 | 96.6 | 0.767 | 0.767 | 0.41 | 1 | 4.3 | 42540 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | 3OJT | 1.42 | 47.95 | 284088 | 14907 | 98.26 | 0.1256 | 0.1238 | 0.1599 | RANDOM | 17.335 |
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] | |
0.05 | -0.11 | 0.06 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_sphericity_free | 27.706 |
r_sphericity_bonded | 8.627 |
r_rigid_bond_restr | 2.699 |
r_mcangle_it | 1.914 |
r_mcbond_it | 1.614 |
r_mcbond_other | 1.612 |
r_angle_refined_deg | 1.379 |
r_angle_other_deg | 0.802 |
r_chiral_restr | 0.089 |
r_bond_refined_d | 0.01 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11579 |
Nucleic Acid Atoms | |
Solvent Atoms | 1680 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
MOLREP | phasing |