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Crystal structure of KDM5B in complex with S49195a.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A1F
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 4.17 70.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.41 α = 90 b = 141.41 β = 90 c = 150.95 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 2016-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.05 64.03 100 18.8 19.6 56258
Highest Resolution Shell 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 2.05 2.1 100 0.125 20.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT NONE 5A1F 2.05 56.742 1.34 56193 2875 99.98 0.1805 0.1794 0.1802 0.2004 0.2002 45.0013
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 5.341 f_angle_d 0.867 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3569 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 68
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling MOLREP phasing