1MKT
CARBOXYLIC ESTER HYDROLASE, 1.72 ANGSTROM TRIGONAL FORM OF THE BOVINE RECOMBINANT PLA2 ENZYME
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 2BPP | RECOMBINANT PLA2 (PDB ENTRY 2BPP) |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 7.2 | CRYSTALS WERE GROWN BY THE VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 75% MPD AND (50%) OF MPD IN THE RESERVOIR, vapor diffusion |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.36 | 48 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 46.78 | α = 90 |
b = 46.78 | β = 90 |
c = 102.89 | γ = 120 |
Symmetry | |
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Space Group | P 31 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1995-10-24 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU R-AXIS II |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.72 | 15 | 79.4 | 0.079 | 3 | 11516 | 1 |
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) | |||||||||||
1.72 | 1.8 | 55 | 0.212 | 1.9 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | RECOMBINANT PLA2 (PDB ENTRY 2BPP) | 1.72 | 8 | 2 | 11337 | 806 | 79 | 0.195 | 0.195 | 0.284 | BY X-PLOR |
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 | 22.7 |
x_angle_deg | 1.6 |
x_improper_angle_d | 1.3 |
x_bond_d | 0.01 |
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 | 957 |
Nucleic Acid Atoms | |
Solvent Atoms | 106 |
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 |