☰ Navigation Tabs
compound 5b 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 1.3 M Na3Citrate, 0.1M HEPES 7.75
Crystal Properties Matthews coefficient Solvent content 3.2 61.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.538 α = 90 b = 110.538 β = 90 c = 131.119 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) 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 1.7 47.86 99.8 0.083 1 30.2 39.6 52543
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 1.7 1.73 0.592
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 1.7 47.86 52483 2645 99.753 0.149 0.1468 0.1525 0.1821 0.1863 36.064
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] 0.749 0.374 0.749 -2.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.231 r_dihedral_angle_3_deg 14.816 r_scangle_it 8.786 r_scangle_other 8.784 r_scbond_it 8.083 r_scbond_other 8.08 r_lrange_other 7.724 r_lrange_it 7.716 r_dihedral_angle_2_deg 7.444 r_dihedral_angle_1_deg 6.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.231 r_dihedral_angle_3_deg 14.816 r_scangle_it 8.786 r_scangle_other 8.784 r_scbond_it 8.083 r_scbond_other 8.08 r_lrange_other 7.724 r_lrange_it 7.716 r_dihedral_angle_2_deg 7.444 r_dihedral_angle_1_deg 6.923 r_rigid_bond_restr 5.495 r_mcangle_other 4.951 r_mcangle_it 4.949 r_mcbond_it 4.658 r_mcbond_other 4.643 r_angle_refined_deg 1.694 r_angle_other_deg 0.565 r_nbd_refined 0.23 r_nbd_other 0.215 r_symmetry_nbd_refined 0.201 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_refined 0.105 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.084 r_chiral_restr_other 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2401 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing