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Structure of compound 1 bound KMT9
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 8 293 1.3 M Na3Citrate, 0.1M Tris ph 8.0
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.344 α = 90 b = 110.344 β = 90 c = 129.875 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 2019-02-11 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) 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 1.46 47.78 99.9 1 1.6 38.9 80857
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 1.46 8 0.579
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.46 47.83 76713 4070 99.94 0.15337 0.15179 0.1833 0.1756 RANDOM 19.019
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.624 r_dihedral_angle_2_deg 10.769 r_dihedral_angle_1_deg 6.337 r_rigid_bond_restr 5.559 r_scangle_other 3.52 r_scbond_it 3.3 r_scbond_other 3.298 r_long_range_B_refined 3.223 r_long_range_B_other 3.223 r_mcangle_it 2.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.624 r_dihedral_angle_2_deg 10.769 r_dihedral_angle_1_deg 6.337 r_rigid_bond_restr 5.559 r_scangle_other 3.52 r_scbond_it 3.3 r_scbond_other 3.298 r_long_range_B_refined 3.223 r_long_range_B_other 3.223 r_mcangle_it 2.205 r_mcangle_other 2.205 r_mcbond_it 1.955 r_mcbond_other 1.951 r_angle_refined_deg 1.762 r_angle_other_deg 0.61 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2401 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing