5JWY
Structure of lipid phosphate phosphatase PgpB complex with PE
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 298 | PEG6000, sodium chloride, ADA |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.21 | 61.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 39.533 | α = 90 |
b = 73.593 | β = 90 |
c = 132.095 | 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 | CCD | MARMOSAIC 225 mm CCD | 2010-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | 0.9794 | SLS | X06SA |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 3.2 | 132.1 | 100 | 0.102 | 25.2 | 14 | 6838 |
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 | 3.2 | 3.37 | 100 | 0.778 | 1 | 14.5 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 3.2 | 132.1 | 6800 | 323 | 99.91 | 0.2691 | 0.2672 | 0.3051 | RANDOM | 93.591 |
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] | |
2.21 | 10.62 | -12.84 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.181 |
r_dihedral_angle_3_deg | 17.087 |
r_dihedral_angle_4_deg | 14.842 |
r_mcangle_it | 7.21 |
r_dihedral_angle_1_deg | 5.545 |
r_mcbond_other | 4.439 |
r_mcbond_it | 4.438 |
r_angle_other_deg | 3.468 |
r_angle_refined_deg | 1.276 |
r_chiral_restr | 0.061 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2104 |
Nucleic Acid Atoms | |
Solvent Atoms | 2 |
Heterogen Atoms | 43 |
Software
Software | |
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Software Name | Purpose |
SCALA | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
PHENIX | phasing |