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Crystal Structure of KDM4A with Compound 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3
Crystal Properties Matthews coefficient Solvent content 2.52 51.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.457 α = 90 b = 101.739 β = 99.51 c = 142.287 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 80 CCD ADSC QUANTUM 315 2012-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D 0.95 APS 14-BM-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.34 140.33 98.7 0.102 12.3 3.8 67709
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.48 0.755
Refinement Statistics 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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5VGI 2.34 140.3 64243 3442 98.66 0.1771 0.174 0.1785 0.2335 0.2372 RANDOM 43.884
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] -0.55 0.73 0.1 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.274 r_dihedral_angle_4_deg 18.08 r_dihedral_angle_3_deg 17.826 r_dihedral_angle_1_deg 6.863 r_angle_refined_deg 1.763 r_angle_other_deg 1.06 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.274 r_dihedral_angle_4_deg 18.08 r_dihedral_angle_3_deg 17.826 r_dihedral_angle_1_deg 6.863 r_angle_refined_deg 1.763 r_angle_other_deg 1.06 r_chiral_restr 0.103 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11267 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 92
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing