2Y8H
STRUCTURE OF THE FIRST GAF DOMAIN E87G MUTANT OF MYCOBACTERIUM TUBERCULOSIS DOSS
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2W3D | PDB ENTRY 2W3D |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 7 | PROTEIN WAS CRYSTALLIZED FROM 17% PEG 3350, 200 MM CALCIUM ACETATE, 100 MM TRIS-HCL, PH 7.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 48.84 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.74 | α = 90 |
b = 86.764 | β = 90 |
c = 100.459 | 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 | 294 | CCD | ADSC CCD | 2009-10-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | PAL/PLS BEAMLINE 4A | PAL/PLS | 4A |
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 | 1.9 | 50 | 99 | 0.1 | 24.8 | 6.8 | 25905 | -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 | 1.9 | 1.93 | 86.2 | 0.32 | 4.4 | 4.6 |
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 2W3D | 1.9 | 31.24 | 24411 | 1313 | 98.48 | 0.21226 | 0.20988 | 0.25585 | RANDOM | 23.348 |
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] | |
0.01 | -0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.655 |
r_dihedral_angle_4_deg | 13.055 |
r_dihedral_angle_3_deg | 12.16 |
r_dihedral_angle_1_deg | 5.495 |
r_scangle_it | 3.152 |
r_scbond_it | 2.003 |
r_angle_refined_deg | 1.428 |
r_mcangle_it | 1.415 |
r_mcbond_it | 0.817 |
r_chiral_restr | 0.089 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2277 |
Nucleic Acid Atoms | |
Solvent Atoms | 308 |
Heterogen Atoms | 87 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data scaling |
AMoRE | phasing |