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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 186)
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 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.711 α = 90 b = 71.711 β = 90 c = 150.832 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 1.24 29.51 98.6 0.072 0.075 0.021 0.999 18.8 11.2 110658
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 1.24 1.26 83.8 0.743 0.853 0.399 0.631 3.8 4538
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 1.24 29.51 105074 5474 98.46 0.1614 0.1605 0.1689 0.1799 0.189 RANDOM 15.216
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] 0.13 0.13 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.469 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 11.522 r_dihedral_angle_1_deg 6.716 r_angle_refined_deg 2.41 r_mcangle_it 2.305 r_mcbond_it 1.638 r_mcbond_other 1.621 r_angle_other_deg 1.17 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.469 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 11.522 r_dihedral_angle_1_deg 6.716 r_angle_refined_deg 2.41 r_mcangle_it 2.305 r_mcbond_it 1.638 r_mcbond_other 1.621 r_angle_other_deg 1.17 r_chiral_restr 0.14 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 r_gen_planes_other 0.003 r_bond_other_d 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