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compound 1b bound KMT9 crystal structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6H1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.1 M Na3Citrate, 0.1M HEPES 7.25
Crystal Properties Matthews coefficient Solvent content 3.17 61.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.516 α = 90 b = 110.516 β = 90 c = 129.837 γ = 120
Symmetry Space Group P 61 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-F 2019-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.467 47.901 99.8 0.095 0.097 0.021 1 26.4 39.4 80097
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 1.47 1.49 4.189 4.331 1.086 0.448 29.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.467 47.901 80029 4033 99.782 0.159 0.1576 0.1538 0.1905 0.1862 24.636
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] -0.3 -0.15 -0.3 0.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.154 r_dihedral_angle_3_deg 14.381 r_rigid_bond_restr 13.962 r_scbond_it 10.385 r_scbond_other 10.381 r_scangle_it 10.284 r_scangle_other 10.281 r_lrange_other 8.843 r_lrange_it 8.838 r_dihedral_angle_2_deg 8.481
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.154 r_dihedral_angle_3_deg 14.381 r_rigid_bond_restr 13.962 r_scbond_it 10.385 r_scbond_other 10.381 r_scangle_it 10.284 r_scangle_other 10.281 r_lrange_other 8.843 r_lrange_it 8.838 r_dihedral_angle_2_deg 8.481 r_mcangle_other 6.652 r_mcangle_it 6.649 r_dihedral_angle_1_deg 6.639 r_mcbond_it 6.123 r_mcbond_other 6.114 r_angle_refined_deg 1.736 r_angle_other_deg 0.606 r_nbd_refined 0.233 r_symmetry_nbd_other 0.183 r_nbd_other 0.177 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.162 r_symmetry_nbd_refined 0.15 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.081 r_chiral_restr_other 0.044 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2407 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing