1A3D
PHOSPHOLIPASE A2 (PLA2) FROM NAJA NAJA VENOM
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1PSH | PDB ENTRY 1PSH |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7.5 | 295.5 | 1.4M (NH4)2SO4, 1% PEG 400, AND 0.1M TRIS PH 7.5 AT 22.5 DEGREES C., temperature 295.5K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.05 | 40 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 69.24 | α = 90 |
b = 69.24 | β = 90 |
c = 69.24 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 | 22 | AREA DETECTOR | XUONG-HAMLIN MULTIWIRE | 1993-01-16 | M |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 1.78 | 23.06 | 98 | 0.06 | 12.6 | 9.7 | 10508 | 2 | 17.8 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.8 | 1.88 | 90.1 | 0.3 | 2 | 8.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 | MOLECULAR REPLACEMENT | POST REFINEMENT | PDB ENTRY 1PSH | 1.8 | 6 | 2 | 10028 | 1031 | 95.2 | 0.175 | 0.175 | 0.23 | RANDOM | 22.8 |
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 | 23.2 |
x_angle_deg | 1.86 |
x_improper_angle_d | 1.66 |
x_bond_d | 0.017 |
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 | 1052 |
Nucleic Acid Atoms | |
Solvent Atoms | 119 |
Heterogen Atoms | 120 |
Software
Software | |
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Software Name | Purpose |
UCSD | data collection |
UCSD | data reduction |
X-PLOR | model building |
X-PLOR | refinement |
UCSD | data scaling |
X-PLOR | phasing |