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Crystal structure of PDE6D KRas peptide complex with Compound-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TB5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M Lithium sulphate, 0.1M Tris pH 8.5 and 20% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.61 52.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.104 α = 90 b = 81.123 β = 90 c = 118.514 γ = 90
Symmetry Space Group C 2 2 21
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 EIGER X 16M 2018-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 Diamond I04-1
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 1.85 40.657 100 0.999 8.4 8.4 32070
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 1.85 1.9 0.88
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5TB5 1.85 40.657 32034 1575 99.906 0.201 0.1993 0.2273 0.2173 31.262
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] 0.019 -0.226 0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.833 r_dihedral_angle_3_deg 16.996 r_dihedral_angle_4_deg 16.271 r_lrange_it 8.79 r_lrange_other 8.789 r_dihedral_angle_1_deg 6.885 r_scangle_it 6.561 r_scangle_other 6.56 r_scbond_it 4.319 r_scbond_other 4.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.833 r_dihedral_angle_3_deg 16.996 r_dihedral_angle_4_deg 16.271 r_lrange_it 8.79 r_lrange_other 8.789 r_dihedral_angle_1_deg 6.885 r_scangle_it 6.561 r_scangle_other 6.56 r_scbond_it 4.319 r_scbond_other 4.318 r_mcangle_it 3.825 r_mcangle_other 3.824 r_mcbond_it 2.893 r_mcbond_other 2.892 r_angle_other_deg 1.434 r_angle_refined_deg 1.379 r_nbd_refined 0.498 r_symmetry_xyhbond_nbd_other 0.388 r_xyhbond_nbd_refined 0.306 r_symmetry_nbd_other 0.297 r_nbd_other 0.289 r_symmetry_nbd_refined 0.228 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.095 r_chiral_restr 0.054 r_chiral_restr_other 0.006 r_bond_refined_d 0.004 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2489 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing