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Crystal Structure of human JMJD2D complexed with KDOAM16
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 30% PEG3350 , 0.1M HEPES pH 7.0 , 0.25M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.28 α = 90 b = 71.28 β = 90 c = 150.36 γ = 90
Symmetry Space Group P 43 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 2012-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.41 50.4 100 0.083 0.024 0.998 18.6 13.1 75484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.41 1.45 99.9 0.722 0.207 0.901 3.7 12.8 5477
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4D6Q 1.41 50.4 71618 3769 99.91 0.1328 0.1311 0.1647 0.186 RANDOM 19.075
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] 0.31 0.31 -0.62
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.731 r_dihedral_angle_2_deg 35.893 r_dihedral_angle_4_deg 22.831 r_dihedral_angle_3_deg 11.962 r_sphericity_bonded 9.883 r_dihedral_angle_1_deg 6.287 r_mcangle_it 2.137 r_rigid_bond_restr 1.734 r_mcbond_it 1.61 r_mcbond_other 1.61
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 36.731 r_dihedral_angle_2_deg 35.893 r_dihedral_angle_4_deg 22.831 r_dihedral_angle_3_deg 11.962 r_sphericity_bonded 9.883 r_dihedral_angle_1_deg 6.287 r_mcangle_it 2.137 r_rigid_bond_restr 1.734 r_mcbond_it 1.61 r_mcbond_other 1.61 r_angle_refined_deg 1.532 r_angle_other_deg 0.99 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2650 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms 91
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction REFMAC phasing