1VKQ
A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | vapor diffusion method | 7.2 | 293 | 50 mM Tris Buffer, 70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2 and 60% MPD in the droplet, pH 7.2, vapor diffusion method, temperature 293.0K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.25 | 45.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 46.05 | α = 90 |
b = 46.05 | β = 90 |
c = 101.58 | 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 | 100 | CCD | MARRESEARCH | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X9A | NSLS | X9A |
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 | 19.96 | 0.059 | 50.1 | 12.1 | 17048 |
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 | 1.66 | 0.284 | 3188 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | SULPHUR-SAS | THROUGHOUT | 1.6 | 19.96 | 17048 | 16184 | 860 | 99.66 | 0.17893 | 0.17703 | 0.21658 | RANDOM | 24.462 |
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] | |
-0.02 | -0.01 | -0.02 | 0.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_1_deg | 5.62 |
r_scangle_it | 4.071 |
r_scbond_it | 2.569 |
r_mcangle_it | 1.671 |
r_angle_refined_deg | 1.536 |
r_mcbond_it | 0.88 |
r_symmetry_vdw_refined | 0.227 |
r_nbd_refined | 0.203 |
r_xyhbond_nbd_refined | 0.173 |
r_symmetry_hbond_refined | 0.123 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 954 |
Nucleic Acid Atoms | |
Solvent Atoms | 189 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
REFMAC | refinement |
SCALEPACK | data scaling |