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Crystal structure of human PLU-1 (JARID1B) in complex with KDM5-C49 (2-(((2-((2-(dimethylamino)ethyl)(ethyl)amino)-2-oxoethyl)amino)methyl) isonicotinic acid).
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 = 141.852 α = 90 b = 141.852 β = 90 c = 151.509 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 2015-01-26 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 1.9 47.71 100 0.1 23.4 22.3 71027 2
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 1.9 2 100 1.5 2.3 22.5
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 1.9 122.85 67433 3534 99.96 0.20046 0.19944 0.2068 0.22039 0.2246 RANDOM 39.632
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] 0.27 0.13 0.27 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.217 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_3_deg 12.448 r_dihedral_angle_1_deg 6.043 r_mcangle_it 3.559 r_scbond_it 2.77 r_mcbond_it 2.268 r_mcbond_other 2.268 r_angle_refined_deg 1.497 r_angle_other_deg 1.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.217 r_dihedral_angle_4_deg 15.976 r_dihedral_angle_3_deg 12.448 r_dihedral_angle_1_deg 6.043 r_mcangle_it 3.559 r_scbond_it 2.77 r_mcbond_it 2.268 r_mcbond_other 2.268 r_angle_refined_deg 1.497 r_angle_other_deg 1.009 r_chiral_restr 0.134 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 3676 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling CCP4-AUTOMR phasing