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Crystal structure of human JMJD2A in complex with compound 43
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OQ7 PDB ENTRY 2OQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 22% PEG3350 -- 0.1M BIS-TRIS PH 7.5 -- 0.25M AMMONIUM SULFATE
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.12 α = 90 b = 149.76 β = 90 c = 57.89 γ = 90
Symmetry Space Group P 21 21 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 2M 2013-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
Data Collection Overall 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 2.39 54 99.5 0.11 12.3 6.6 35446 2 39.96
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 2.39 2.45 99.9 0.83 2.4 7
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 2OQ7 2.39 53.996 1.36 35393 1489 99.32 0.1855 0.1828 0.1996 0.2445 0.2541
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 13.515 f_angle_d 1.084 f_chiral_restr 0.043 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5587 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHENIX phasing