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compound 3b 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 1.2 M Na3Citrate, 0.1M Tris 7.5
Crystal Properties Matthews coefficient Solvent content 3.17 61.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.293 α = 90 b = 110.293 β = 90 c = 130.473 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 2019-02-08 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) 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 1.39 47.76 99.9 0.093 1 28.7 39 93637
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.42 0.613
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.392 47.76 93564 4774 99.878 0.152 0.1501 0.1791 0.1643 22.124
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] -0.093 -0.047 -0.093 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.266 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_2_deg 8.557 r_scbond_it 7.208 r_scbond_other 7.206 r_scangle_it 7.203 r_scangle_other 7.201 r_lrange_other 7.04 r_lrange_it 7.03 r_rigid_bond_restr 6.982
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.266 r_dihedral_angle_3_deg 14.282 r_dihedral_angle_2_deg 8.557 r_scbond_it 7.208 r_scbond_other 7.206 r_scangle_it 7.203 r_scangle_other 7.201 r_lrange_other 7.04 r_lrange_it 7.03 r_rigid_bond_restr 6.982 r_dihedral_angle_1_deg 6.414 r_mcangle_it 5.397 r_mcangle_other 5.396 r_mcbond_it 5.311 r_mcbond_other 5.311 r_angle_refined_deg 1.744 r_angle_other_deg 0.604 r_nbd_refined 0.233 r_symmetry_nbd_refined 0.214 r_nbd_other 0.205 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.137 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2418 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing