4OW8
Crystal structure of kinase domain of PknA from Mtb
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1O6Y |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293 | 0.25 M NaCl, 1.1 M (NH4)2SO4, 0.1 M Bis-Tris (pH 6.5) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.07 | 40.5 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 54.139 | α = 90 |
b = 58.412 | β = 96.2 |
c = 78.867 | γ = 90 |
Symmetry | |
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Space Group | I 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 | 100 | IMAGE PLATE | MAR scanner 345 mm plate | Varimax Optics | 2013-10-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.03 | 46.84 | 99.8 | 0.057 | 22.9 | 6 | 15916 | 15916 | -3 | 19.1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.03 | 2.14 | 98.8 | 0.238 | 10.3 | 5.4 |
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 | 1O6Y | 2.03 | 46.84 | 15124 | 791 | 99.82 | 0.22846 | 0.22601 | 0.2749 | RANDOM | 23.41 |
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 | 0.99 | 0.15 | -0.2 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.027 |
r_dihedral_angle_4_deg | 20.31 |
r_dihedral_angle_3_deg | 16.706 |
r_dihedral_angle_1_deg | 6.225 |
r_long_range_B_refined | 3.64 |
r_long_range_B_other | 3.636 |
r_mcangle_it | 2.146 |
r_mcangle_other | 2.145 |
r_scangle_other | 2.033 |
r_angle_refined_deg | 1.38 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2037 |
Nucleic Acid Atoms | |
Solvent Atoms | 86 |
Heterogen Atoms | 11 |
Software
Software | |
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Software Name | Purpose |
XDS | data scaling |
REFMAC | refinement |
SCALA | data scaling |
PHASER | phasing |