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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 91)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D6R 4D6R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.297 α = 90 b = 71.297 β = 90 c = 150.083 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 6M 2012-12-15 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97630 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.38 29.35 99.7 0.179 0.186 0.051 0.998 15.5 12.7 16149
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.38 2.49 97.7 0.917 0.957 0.267 0.873 12.2 1881
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 FOURIER SYNTHESIS THROUGHOUT 4D6R 2.38 29.35 15317 774 99.62 0.1491 0.1462 0.1525 0.206 0.2064 RANDOM 31.926
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] 1.4 1.4 -2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 13.22 r_dihedral_angle_1_deg 6.277 r_mcangle_it 3.338 r_mcbond_it 2.189 r_mcbond_other 2.175 r_angle_refined_deg 1.538 r_angle_other_deg 0.989 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.265 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 13.22 r_dihedral_angle_1_deg 6.277 r_mcangle_it 3.338 r_mcbond_it 2.189 r_mcbond_other 2.175 r_angle_refined_deg 1.538 r_angle_other_deg 0.989 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2664 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing