1KP4
CALCIUM-BOUND FORM OF PROKARYOTIC PHOSPHOLIPASE A2
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1FAZ | PDB ENTRY 1FAZ |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 297 | MPD, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.02 | 47.53 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 38.28 | α = 90 |
b = 54.25 | β = 90.2 |
c = 30.65 | γ = 90 |
Symmetry | |
---|---|
Space Group | P 1 21 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 292 | IMAGE PLATE | RIGAKU RAXIS IIC | mirrors | 1999-03-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU RU300 | 1.5418 |
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 | 1.6 | 100 | 73.2 | 0.065 | 11.2 | 2.37 | 14730 | 12820 | 2 | 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) | |||||||||||
1.6 | 1.7 | 48 | 0.283 | 2.41 | 1325 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | AB INITIO | PDB ENTRY 1FAZ | 1.6 | 5 | 12244 | 12244 | 76.3 | 0.1496 | 0.1496 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
1047 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.048 |
s_zero_chiral_vol | 0.045 |
s_similar_adp_cmpnt | 0.041 |
s_angle_d | 0.023 |
s_from_restr_planes | 0.0208 |
s_bond_d | 0.008 |
s_anti_bump_dis_restr | 0.007 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 958 |
Nucleic Acid Atoms | |
Solvent Atoms | 88 |
Heterogen Atoms | 1 |
Software
Software | |
---|---|
Software Name | Purpose |
X-PLOR | model building |
SHELXL-97 | refinement |
X-PLOR | phasing |