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PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM010032a
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 55.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.37 α = 90 b = 93.59 β = 107.85 c = 93.58 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 1.66 89.08 99.1 0.075 0.089 0.048 0.997 8.8 3.4 109887
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 1.66 1.7 99 1.13 1.344 0.718 0.467 3.4 8144
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 1.66 89.08 104305 5558 98.96 0.1815 0.1803 0.1951 0.2052 0.2182 RANDOM 31.447
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] 1.57 -0.05 -1.21 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.433 r_dihedral_angle_4_deg 21.174 r_dihedral_angle_3_deg 14.702 r_dihedral_angle_1_deg 7.402 r_mcangle_it 4.667 r_mcbond_other 3.007 r_mcbond_it 3 r_angle_refined_deg 1.716 r_angle_other_deg 1.356 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.433 r_dihedral_angle_4_deg 21.174 r_dihedral_angle_3_deg 14.702 r_dihedral_angle_1_deg 7.402 r_mcangle_it 4.667 r_mcbond_other 3.007 r_mcbond_it 3 r_angle_refined_deg 1.716 r_angle_other_deg 1.356 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5510 Nucleic Acid Atoms Solvent Atoms 696 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing