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Methyltransferase domain of human suppressor of variegation 3-9 homolog 2 (SUV39H2) in complex with OTS186935 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R3A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% PEG3350, 0.2M NH4Formate
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.701 α = 90 b = 63.388 β = 113.17 c = 65.616 γ = 90
Symmetry Space Group C 1 2 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 EIGER X 16M 2019-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 50 97.9 0.14 0.166 0.088 6.9 3.3 21217
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 2.4 2.44 98.4 0.778 0.931 0.503 0.703 3.2
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 2R3A 2.4 50.01 20360 856 97.53 0.2147 0.2123 0.2159 0.2667 0.2684 RANDOM 42.46
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] 1.88 1.04 -3.71 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.949 r_dihedral_angle_4_deg 17.074 r_dihedral_angle_3_deg 13.489 r_dihedral_angle_1_deg 6.59 r_angle_refined_deg 1.08 r_angle_other_deg 0.823 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.949 r_dihedral_angle_4_deg 17.074 r_dihedral_angle_3_deg 13.489 r_dihedral_angle_1_deg 6.59 r_angle_refined_deg 1.08 r_angle_other_deg 0.823 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3673 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-3000 data processing