7EZZ
Crystal structure of Salmonella typhi outer membrane phospholipase (OMPLA) dimer with bound calcium
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1QD6 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7 | 293.15 | 0.1 M sodium iodide, 0.1 M sodium phosphate (pH 7.0), and 33% v/v PEG 300 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.18 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.584 | α = 90 |
b = 83.448 | β = 90 |
c = 95.644 | 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 | 100 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2014-01-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E+ SUPERBRIGHT | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | 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 | 2.654 | 62.879 | 95.6 | 0.249 | 0.271 | 0.106 | 0.991 | 7.4 | 6.3 | 17368 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.654 | 2.713 | 96.6 | 0.931 | 1.014 | 0.396 | 0.721 | 6 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | 1QD6 | 2.76 | 47.87 | 16069 | 802 | 99.8 | 0.2266 | 0.2244 | 0.2717 | RANDOM | 29.007 |
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] | |
4.66 | -2.63 | -2.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.299 |
r_dihedral_angle_3_deg | 16.673 |
r_dihedral_angle_4_deg | 16.219 |
r_dihedral_angle_1_deg | 6.806 |
r_angle_refined_deg | 1.48 |
r_chiral_restr | 0.105 |
r_gen_planes_refined | 0.008 |
r_bond_refined_d | 0.007 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4077 |
Nucleic Acid Atoms | |
Solvent Atoms | 54 |
Heterogen Atoms | 96 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
autoPROC | data processing |
autoPROC | data scaling |
PHENIX | phasing |
Coot | model building |