2CZ8
Crystal Structure of tt0972 protein from Thermus thermophilus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1MOG | pdb entry 1mog |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 5.8 | 291 | SODIUM, potassium phosphate, pH 5.8, MICRO BATCH, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.6 | 51.8 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 66.36 | α = 90 |
b = 66.36 | β = 90 |
c = 124.566 | γ = 120 |
Symmetry | |
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Space Group | P 3 |
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 | mirrors | 2005-05-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL26B2 | 0.8 | SPring-8 | BL26B2 |
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 | 1.25 | 50 | 99 | 0.057 | 24.7 | 3.9 | 96989 | 96989 | 15.2 |
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 | 1.25 | 1.27 | 98.1 | 0.49 | 3.1 | 3.9 | 8276 |
Refinement
Statistics | |||||||||||||||||||
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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 | pdb entry 1mog | 1.5 | 29.28 | 96989 | 96989 | 4913 | 98.7 | 0.205 | 0.205 | 0.229 | RANDOM | 19.7 |
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] | |
-0.16 | 0.32 | -0.16 | 0.33 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
c_dihedral_angle_d | 22.2 |
c_scangle_it | 3.07 |
c_scbond_it | 2.06 |
c_mcangle_it | 2.03 |
c_angle_deg | 1.5 |
c_mcbond_it | 1.26 |
c_improper_angle_d | 0.78 |
c_bond_d | 0.008 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4256 |
Nucleic Acid Atoms | |
Solvent Atoms | 627 |
Heterogen Atoms | 473 |
Software
Software | |
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Software Name | Purpose |
CNS | refinement |
BSS | data collection |
SCALEPACK | data scaling |
MOLREP | phasing |