1JIA
STRUCTURE OF A BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS AT 2.13A RESOLUTION
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 9.5 | THE PROTEIN SOLUTIONS CONTAINED 10MM CA2+, 0.1M NACL, 5% PEG 4K IN 0.01M CHESS BUFFER (PH 9.5) AND AN ENZYME CONCENTRATION OF 11MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 10% PEG 4K IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.09 | 37 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 97.13 | α = 90 |
b = 103.69 | β = 90 |
c = 23.27 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | 280 | AREA DETECTOR | SIEMENS-NICOLET X200B | 1995-05-27 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RUH2R |
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 | 2.13 | 40 | 86.1 | 0.0459 | 31.2 | 2.5 | 12001 | 26.24 |
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) | |||||||||||
2.13 | 2.23 | 46.28 | 0.176 | 4.9 | 1.6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | STRUCTURE REFINEMENT | FULL REFINEMENT CONSISTING OF INITIAL MINIMIZATION, SLOW COOLING-SA 3000K, POSITIONAL AND B-FACTOR REFINEMENT. | 2.13 | 6 | 3 | 10174 | 1063 | 77.8 | 0.152 | 0.152 | 0.255 | RANDOM | 25.41 |
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 | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 23.4 |
x_angle_deg | 2.72 |
x_improper_angle_d | 1.29 |
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 | 1916 |
Nucleic Acid Atoms | |
Solvent Atoms | 190 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
XENGEN | data collection |
XENGEN | data reduction |
X-PLOR | model building |
X-PLOR | refinement |
XENGEN | data scaling |
X-PLOR | phasing |