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Crystal structure of human JMJD2A in complex with compound KDOAM20A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4URA PDB ENTRY 4URA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.9 0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.6 52.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.346 α = 90 b = 103.509 β = 106.37 c = 157.103 γ = 90
Symmetry Space Group P 1 21 1
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 MIRRORS 2014-12-16 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 2.44 106.83 98.7 0.09 11.6 3.6 438854 2 35.69
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 2.44 2.57 99.4 0.56 2.3 3.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4URA 2.44 85.327 1.34 125508 98.45 0.1955 0.2001 0.2289 0.2315
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 13.91 f_angle_d 1.136 f_chiral_restr 0.042 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21899 Nucleic Acid Atoms Solvent Atoms 891 Heterogen Atoms 207
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing