2GJU
Crystal structure of hypothetical protein PH1004 from Pyrococcus horikoshii OT3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 291 | 0.05M Potassium dihydrogen phosphate, 10% PEG 8000, MICROBATCH, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.1 | 60.26 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 99.742 | α = 90 |
b = 129.571 | β = 104.46 |
c = 113.557 | 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 | 103 | CCD | RIGAKU JUPITER 210 | MIRRORS | 2005-12-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.0000 | SPring-8 | BL26B1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2 | 40 | 98.3 | 0.095 | 0.086 | 8.5 | 4 | 93428 | 91840 | 14.3 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2 | 2.07 | 95.7 | 0.281 | 0.256 | 3.6 | 3.7 | 8949 |
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 (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1NNW | 2 | 39.43 | 93810 | 91840 | 4608 | 97.9 | 0.197 | 0.197 | 0.214 | RANDOM | 25.9 |
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] | |
-2.33 | 2.06 | 6.36 | -4.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 24.4 |
c_angle_deg | 1.5 |
c_improper_angle_d | 1.05 |
c_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8088 |
Nucleic Acid Atoms | |
Solvent Atoms | 1039 |
Heterogen Atoms | 39 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
CrystalClear | data reduction |
HKL-2000 | data scaling |
SOLVE | phasing |