3K5K
Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2O8J | PDB ENTRY 2O8J |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 293 | 0.2M sodium fluoride, 0.1M Bis-Tris phosphate pH 6.0, 18% polyethylene glycol 3350 and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.46 | 49.97 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 56.674 | α = 90 |
b = 78.074 | β = 91.81 |
c = 72.507 | 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 | IMAGE PLATE | RIGAKU RAXIS HTC | VeriMax HR | 2009-09-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E SUPERBRIGHT | 1.54 |
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 | 1.7 | 50 | 97.1 | 0.044 | 0.044 | 13 | 5.8 | 67707 | 67707 | 30.2 |
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) | ||||||||||
1.7 | 1.73 | 67.6 | 0.727 | 0.727 | 1.26 | 2.6 | 2369 |
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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB ENTRY 2O8J | 1.7 | 29.58 | 66303 | 1372 | 96.95 | 0.21061 | 0.21061 | 0.2095 | 0.2643 | RANDOM | 33.946 |
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] | |
-2.52 | 1.75 | 0.03 | 2.6 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.579 |
r_dihedral_angle_4_deg | 13.739 |
r_dihedral_angle_3_deg | 11.969 |
r_dihedral_angle_1_deg | 5.569 |
r_scangle_it | 2.875 |
r_scbond_it | 1.841 |
r_mcangle_it | 1.393 |
r_angle_refined_deg | 1.309 |
r_mcbond_it | 0.755 |
r_chiral_restr | 0.082 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4190 |
Nucleic Acid Atoms | |
Solvent Atoms | 459 |
Heterogen Atoms | 136 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
PHASER | phasing |
REFMAC | refinement |
Coot | model building |
HKL-2000 | data reduction |
HKL-2000 | data scaling |