☰ Navigation Tabs
Crystal structure of the catalytic domain of human JARID1B in complex with Maybridge fragment 3-pyridin-3-ylaniline (N05798a) (ligand modelled based on PANDDA event map)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A3P PDB ENTRY 5A3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.1M HEPES PH 7.5 -- 0.8M POTASSIUM PHOSPHATE DIBASIC -- 0.8M SODIUM PHOSPHATE MONOBASIC
Crystal Properties Matthews coefficient Solvent content 2.11 41.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.79 α = 90 b = 141.79 β = 90 c = 152.3 γ = 120
Symmetry Space Group P 65 2 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 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.18 64.72 100 0.2 12.9 19.8 47615 1.2 41.31
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.24 100 1.5 1.2 19.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 5A3P 2.18 46.412 1.34 47547 2432 99.98 0.1885 0.1867 0.1897 0.2216 0.223
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.175 f_angle_d 1.133 f_chiral_restr 0.046 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3671 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 110
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling DIMPLE phasing