3TNB
Crystal structure of GkaP mutant G209D/R230H from Geobacillus kaustophilus HTA426
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ORW | PDB ENTRY 3ORW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.3 | 287 | 13% PEG 8000, 8% ethylene glycol, 2% glycerol, 0.05M sodium hepes pH7.3, vapor diffusion, hanging drop, temperature 287K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.51 | 50.95 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 51.293 | α = 90 |
b = 88.8 | β = 98.86 |
c = 89.314 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 | RAYONIX MX-225 | 2010-03-15 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 1.000 | SSRF | BL17U |
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 | 1.6 | 50 | 99.7 | 0.056 | 12.9 | 7.2 | 103659 |
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 | 1.6 | 1.66 | 100 | 0.459 | 7 | 10359 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 3ORW | 1.6 | 50 | 103600 | 5175 | 99.68 | 0.1781 | 0.1774 | 0.1919 | RANDOM | 24.3437 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
-0.43 | -1.05 | 0.01 | 0.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.906 |
r_dihedral_angle_4_deg | 17.953 |
r_dihedral_angle_3_deg | 13.526 |
r_dihedral_angle_1_deg | 5.565 |
r_scangle_it | 2.488 |
r_scbond_it | 1.402 |
r_angle_refined_deg | 1.071 |
r_mcangle_it | 1.001 |
r_mcbond_it | 0.521 |
r_chiral_restr | 0.074 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5102 |
Nucleic Acid Atoms | |
Solvent Atoms | 709 |
Heterogen Atoms | 4 |
Software
Software | |
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Software Name | Purpose |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |