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PanDDA analysis group deposition -- Crystal Structure of JMJD1B in complex with FM001568a
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 2.79 55.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.69 α = 90 b = 93.68 β = 107.81 c = 93.32 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 1.9 54.93 99.2 0.086 0.102 0.054 0.998 11.3 3.4 73760
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 1.9 1.95 99.2 1.109 1.312 0.693 0.519 3.5 5431
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 1.9 54.99 70067 3669 99.04 0.1822 0.1802 0.1946 0.2194 0.2314 RANDOM 35.955
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] 1.96 -0.08 -2.57 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.056 r_dihedral_angle_4_deg 17.503 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 7.494 r_mcangle_it 4.514 r_mcbond_other 2.868 r_mcbond_it 2.858 r_angle_refined_deg 1.561 r_angle_other_deg 1.268 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.056 r_dihedral_angle_4_deg 17.503 r_dihedral_angle_3_deg 15.034 r_dihedral_angle_1_deg 7.494 r_mcangle_it 4.514 r_mcbond_other 2.868 r_mcbond_it 2.858 r_angle_refined_deg 1.561 r_angle_other_deg 1.268 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5506 Nucleic Acid Atoms Solvent Atoms 695 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing