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Crystal structure of human PLU-1 (JARID1B) in complex with KDOAM25a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB PDB ENTRY 51AF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1M HEPES PH 8.0, 0.8M POTASSIUM PHOSPHATE-DIBASIC, 0.8M SODIUM PHOSPHATE MONOBASIC
Crystal Properties Matthews coefficient Solvent content 2.07 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.874 α = 90 b = 141.874 β = 90 c = 151.865 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 MIRRORS 2015-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 19.81 99.3 0.08 21.7 12.6 60715 3.5
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 2.11 95.8 0.64 3.5 8.9
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 51AF 2 122.87 57644 3018 99.14 0.18382 0.18281 0.1907 0.20335 0.2071 RANDOM 36.565
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] 0.43 0.21 0.43 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.71 r_dihedral_angle_4_deg 14.753 r_dihedral_angle_3_deg 12.656 r_dihedral_angle_1_deg 6.204 r_mcangle_it 3.228 r_scbond_it 2.476 r_mcbond_other 2.024 r_mcbond_it 2.023 r_angle_refined_deg 1.358 r_angle_other_deg 0.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.71 r_dihedral_angle_4_deg 14.753 r_dihedral_angle_3_deg 12.656 r_dihedral_angle_1_deg 6.204 r_mcangle_it 3.228 r_scbond_it 2.476 r_mcbond_other 2.024 r_mcbond_it 2.023 r_angle_refined_deg 1.358 r_angle_other_deg 0.947 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3656 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling CCP4-AUTOMR phasing