2ZVJ
Crystal structures of rat Catechol-O-Methyltransferase complexed with coumarine-based inhibitor
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1VID | PDB entry 1VID |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | 0.2M (NH4)2SO4, 30% PEG 8000, 0.1M Tris pH7.5, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.47 | 50.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 50.448 | α = 90 |
b = 50.448 | β = 90 |
c = 167.626 | γ = 120 |
Symmetry | |
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Space Group | P 32 2 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 | CCD | RIGAKU JUPITER 210 | 2004-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL32B2 | 1.0 | SPring-8 | BL32B2 |
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 | 2.3 | 42.3 | 99.6 | 0.074 | 0.068 | 16.7 | 6.8 | 11635 | 11591 | 49.5 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.3 | 2.42 | 100 | 0.181 | 8.2 | 7.2 | 1644 |
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 | PDB entry 1VID | 2.3 | 42.3 | 10454 | 1134 | 99.64 | 0.2187 | 0.21147 | 0.28646 | RANDOM | 41.807 |
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] | |
2.22 | 1.11 | 2.22 | -3.32 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 39.27 |
r_dihedral_angle_4_deg | 19.738 |
r_dihedral_angle_3_deg | 17.589 |
r_dihedral_angle_1_deg | 5.777 |
r_scangle_it | 2.829 |
r_scbond_it | 1.798 |
r_angle_refined_deg | 1.667 |
r_mcangle_it | 1.564 |
r_mcbond_it | 0.933 |
r_nbtor_refined | 0.31 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1672 |
Nucleic Acid Atoms | |
Solvent Atoms | 73 |
Heterogen Atoms | 47 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
BBS | data collection |
MOSFLM | data reduction |
SCALA | data scaling |
AMoRE | phasing |