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PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with XS039080d
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RBJ 6RBJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 0.1M bis-tris pH 5.5 21% PEG3350 0.3M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.52 α = 90 b = 93.75 β = 108.18 c = 93.605 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 100 PIXEL DECTRIS PILATUS 2M 2015-09-30 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.92819 Diamond I02
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 1.95 93.75 99.1 0.078 0.093 0.049 0.997 10.7 3.4 68122
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 1.95 2 99.4 1.173 1.386 0.731 0.568 3.5 5046
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 6RBJ 1.95 88.93 64706 3393 98.96 0.1849 0.1828 0.2016 0.2248 0.2381 RANDOM 41.547
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] 2.25 -0.49 -2.28 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.808 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_3_deg 15.919 r_dihedral_angle_1_deg 7.501 r_mcangle_it 5.233 r_mcbond_other 3.197 r_mcbond_it 3.183 r_angle_refined_deg 1.558 r_angle_other_deg 1.247 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.808 r_dihedral_angle_4_deg 19.414 r_dihedral_angle_3_deg 15.919 r_dihedral_angle_1_deg 7.501 r_mcangle_it 5.233 r_mcbond_other 3.197 r_mcbond_it 3.183 r_angle_refined_deg 1.558 r_angle_other_deg 1.247 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5506 Nucleic Acid Atoms Solvent Atoms 683 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing