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Crystal structure of the catalytic domain of human JARID1B in complex with 3D fragment 3-Amino-4-methyl-1,3-dihydro-2H-indol-2-one (N10042a)
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 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.01 α = 90 b = 142.01 β = 90 c = 152.2 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 2M 2015-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 2.06 76.1 100 0.1 18.6 19.8 56377 1.4 45.36
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 2.06 2.11 100 1.5 1.4 20.5
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 2.06 71.005 1.34 56312 2834 99.99 0.1954 0.1937 0.202 0.2274 0.2335
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 13.741 f_angle_d 1.134 f_chiral_restr 0.051 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3681 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling DIMPLE phasing