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Crystal structure of KDM5B in complex with KDOPZ29a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES pH 7.5, 0.8M Pottassium Phosphate-dibasic, 0.8M Sodium Phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 4.28 71.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.38 α = 90 b = 143.38 β = 90 c = 153.82 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.83 124.17 100 0.101 1 19.1 20 82282
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.88 100 2.858 0.604 1.3 20.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION NONE 1.88 65.384 1.34 82204 4063 99.99 0.1969 0.1957 0.1979 0.2209 0.2219 43.3288
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.405 f_angle_d 0.866 f_chiral_restr 0.056 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3572 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 73
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling MOLREP phasing