1VBK
Crystal structure of PH1313 from Pyrococcus horikoshii Ot3
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.4 | 291 | MRD, pH 5.4, MICROBATCH, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.33 | 46.87 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 71.743 | α = 90 |
b = 71.164 | β = 90 |
c = 141.774 | 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 V | 2003-11-30 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | 100 | IMAGE PLATE | RIGAKU RAXIS V | 2004-02-08 |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 1.00000 | SPring-8 | BL26B1 |
2 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B1 | 0.97906 | 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 | 1.9 | 40 | 99.9 | 0.077 | 0.072 | 9 | 5.7 | 57832 | 57832 | 22.27 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 1.9 | 1.97 | 100 | 0.538 | 0.489 | 3.81 | 5.7 | 5719 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | 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 | SAD | THROUGHOUT | 1.9 | 39.47 | 57762 | 57762 | 2880 | 99.5 | 0.203 | 0.203 | 0.199 | 0.222 | RANDOM | 28.1 |
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] | |
-1.45 | 9.1 | -7.65 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_angle_deg | 1.2 |
c_bond_d | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4871 |
Nucleic Acid Atoms | |
Solvent Atoms | 637 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
SCALEPACK | data scaling |
SOLVE | phasing |
CNS | refinement |
HKL-2000 | data reduction |