1KVY
CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT D49E COORDINATED TO CALCIUM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MKT | WILD TYPE, PDB ENTRY 1MKT |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | CRYSTALS WERE GROWN OVER A PERIOD OF ELEVEN MONTHS USING THE HANGING DROP VAPOR DIFFUSION METHOD BY EMPLOYING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (20 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.5 (MICRO)L OF 75% MPD IN THE DROPLET. THE RESERVOIR CONTAINED (55%) OF MPD., vapor diffusion - hanging drop |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 47.94 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.87 | α = 90 |
b = 46.87 | β = 90 |
c = 103.04 | γ = 120 |
Symmetry | |
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Space Group | P 31 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 | 291 | IMAGE PLATE | RIGAKU RAXIS IIC | 1996-08-02 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU R-AXIS II |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.9 | 10 | 92 | 0.061 | 5 | 9912 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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) | |||||||||||
1.9 | 1.99 | 79 | 0.225 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | THE HIGH RESOLUTION ATOMIC COORDINATES OF THE WILD TYPE (PDB ENTRY 1MKT) WERE USED AS THE STARTING MODEL FOR FURTHER REFINEMENT | WILD TYPE, PDB ENTRY 1MKT | 1.9 | 10 | 2 | 9903 | 688 | 92 | 0.198 | 0.198 | 0.277 | X-PLOR METHOD |
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] | |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 23.1 |
x_angle_deg | 1.73 |
x_improper_angle_d | 1.2 |
x_bond_d | 0.013 |
x_bond_d_na | |
x_bond_d_prot | |
x_angle_d | |
x_angle_d_na | |
x_angle_d_prot | |
x_angle_deg_na |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 958 |
Nucleic Acid Atoms | |
Solvent Atoms | 70 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
R-AXIS | data collection |
R-AXIS | data reduction |
X-PLOR | model building |
X-PLOR | refinement |
R-AXIS | data scaling |
X-PLOR | phasing |