5VMP
Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3PDQ |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION | 293 | 22% PEG4K, 100mM HEPES pH 7.5 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.57 | 52.07 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 58.14 | α = 90 |
b = 101.429 | β = 99.85 |
c = 142.673 | 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 | 77 | CCD | ADSC QUANTUM 210 | 2016-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 17-ID | 1.0 | APS | 17-ID |
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 | 2.48 | 50 | 99 | 0.127 | 5.7 | 3.7 | 57177 |
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 | 2.48 | 2.57 | 99.8 | 0.664 | 3.7 |
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 | 3PDQ | 2.48 | 50 | 54229 | 2904 | 98.68 | 0.1965 | 0.1931 | 0.2599 | RANDOM | 41.597 |
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] | |
-1.09 | -1.16 | 1.22 | 0.26 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.765 |
r_dihedral_angle_4_deg | 19.483 |
r_dihedral_angle_3_deg | 16.423 |
r_dihedral_angle_1_deg | 6.685 |
r_angle_refined_deg | 1.635 |
r_angle_other_deg | 1.013 |
r_chiral_restr | 0.095 |
r_bond_refined_d | 0.013 |
r_gen_planes_refined | 0.007 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 11267 |
Nucleic Acid Atoms | |
Solvent Atoms | 244 |
Heterogen Atoms | 100 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data collection |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
MOLREP | phasing |