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SETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O9S PDB ENTRY 1O9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 23% PEG 3500, 0.2 M Lithium Sulfate, 0.1 M BisTris pH 6.5, vapor diffusion hanging drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.66 53.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.742 α = 83.33 b = 57.984 β = 71.42 c = 64.932 γ = 70.93
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2012-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03320 APS 23-ID-D
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 1.896 50 95.3 0.061 38.2 5.6 45882 45882 22.1
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 1.896 1.93 80.6 0.224 4.8 1939
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1O9S 1.896 30.75 45882 45881 1454 94.78 0.2121 0.2121 0.2113 0.2085 0.2366 0.2362 RANDOM 30.5528
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] 0.46 0.59 -1.54 0.16 -2.99 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_4_deg 7.263 r_dihedral_angle_1_deg 5.583 r_scangle_it 2.404 r_scbond_it 1.476 r_angle_refined_deg 1.097 r_mcangle_it 1.063 r_mcbond_it 0.567 r_chiral_restr 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.745 r_dihedral_angle_3_deg 11.943 r_dihedral_angle_4_deg 7.263 r_dihedral_angle_1_deg 5.583 r_scangle_it 2.404 r_scbond_it 1.476 r_angle_refined_deg 1.097 r_mcangle_it 1.063 r_mcbond_it 0.567 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3772 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 147
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction JBluIce-EPICS data collection HKL-2000 data reduction PHASES phasing