3QJG
Epidermin biosynthesis protein EpiD from Staphylococcus aureus
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 289 | 0.1 M Bis-Tris, 20% PEG-MME-5000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.25 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 160.991 | α = 90 |
b = 111.256 | β = 97.25 |
c = 154.569 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
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 | ADSC QUANTUM 210r | 2010-08-12 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-BM | 0.9792 | APS | 19-BM |
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 | 2.04 | 45.8 | 95.3 | 0.116 | 8.1 | 3.9 | 162302 | 162302 | 33.7 |
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) | |||||||||||
2.04 | 2.09 | 74.4 | 0.481 | 2.08 | 2.5 | 6320 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1G5Q | 2.04 | 45.8 | 162164 | 162164 | 8177 | 94.99 | 0.211 | 0.211 | 0.2082 | 0.2626 | RANDOM | 32.7319 |
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] | |
5.66 | 0.65 | -1.83 | -3.67 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 41.908 |
r_dihedral_angle_4_deg | 18.385 |
r_dihedral_angle_3_deg | 16.314 |
r_dihedral_angle_1_deg | 6.221 |
r_scangle_it | 3.326 |
r_scbond_it | 2.169 |
r_angle_refined_deg | 1.629 |
r_mcangle_it | 1.289 |
r_angle_other_deg | 0.962 |
r_mcbond_it | 0.755 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 16396 |
Nucleic Acid Atoms | |
Solvent Atoms | 1504 |
Heterogen Atoms | 378 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
SBC-Collect | data collection |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |
HKL-3000 | phasing |