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PanDDA analysis group deposition -- Crystal Structure of JMJD2D after initial refinement with no ligand modelled (structure 109)
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 2.23 44.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.845 α = 90 b = 70.845 β = 90 c = 149.463 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 29.17 98.4 0.186 0.194 0.054 0.997 15 12.6 15838
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 2.47 86.6 0.811 0.847 0.239 0.848 11.5 1533
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 29.17 15020 761 98.39 0.1624 0.1592 0.1625 0.2273 0.2271 RANDOM 27.848
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] 0.51 0.51 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.29 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_1_deg 6.615 r_mcangle_it 3.813 r_mcbond_it 2.442 r_mcbond_other 2.431 r_angle_refined_deg 1.651 r_angle_other_deg 1.029 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.29 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 13.559 r_dihedral_angle_1_deg 6.615 r_mcangle_it 3.813 r_mcbond_it 2.442 r_mcbond_other 2.431 r_angle_refined_deg 1.651 r_angle_other_deg 1.029 r_chiral_restr 0.1 r_bond_refined_d 0.015 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 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