4EGD
1.85 Angstrom crystal structure of native hypothetical protein SAOUHSC_02783 from Staphylococcus aureus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4EG9 | PDB ENTRY 4EG9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6 | 295 | 7.3 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, screen: PACT, A3, 0.1 M SPG buffer, pH 6.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.95 | 37.02 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.231 | α = 90 |
b = 88.782 | β = 90 |
c = 121.622 | 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 300 mm CCD | Mirrors | 2011-11-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-D | 0.99984 | APS | 21-ID-D |
Data Collection
Overall | |||||||||||||||||||
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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 | 1.85 | 30 | 99.5 | 0.074 | 24.9 | 7.2 | 41503 | 41503 | -3 | 22.9 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.85 | 1.88 | 90.8 | 0.579 | 2.9 | 6.2 | 1842 |
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 | PDB ENTRY 4EG9 | 1.85 | 29.93 | 39354 | 39354 | 2084 | 99.61 | 0.17017 | 0.17017 | 0.1677 | 0.21527 | RANDOM | 25.515 |
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] | |
-0.63 | -2 | 2.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.079 |
r_dihedral_angle_4_deg | 15.904 |
r_dihedral_angle_3_deg | 12.647 |
r_scangle_it | 7.002 |
r_dihedral_angle_1_deg | 5.343 |
r_scbond_it | 4.781 |
r_mcangle_it | 3.331 |
r_mcbond_it | 2.225 |
r_angle_refined_deg | 1.98 |
r_angle_other_deg | 0.966 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3656 |
Nucleic Acid Atoms | |
Solvent Atoms | 291 |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
Blu-Ice | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |