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Crystal structure of the high affinity KRas mutant PDE6D complex
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 Ammonium sulphate, 0.1 M tri sodium citrate pH 5.6, 15 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.88 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.086 α = 82.771 b = 57.925 β = 81.709 c = 78.913 γ = 68.447
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 6M 2017-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 2.238 53.706 94.7 0.995 6.1 1.7 37781
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 2.24 2.3 0.742
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5TB5 2.238 53.706 37435 1774 93.496 0.202 0.1994 0.202 0.2545 0.2521 46.809
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] -0.621 -0.994 -0.933 0.469 0.805 -0.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 18.934 r_dihedral_angle_3_deg 18.179 r_lrange_it 9.087 r_lrange_other 9.086 r_scangle_it 7.043 r_scangle_other 7.042 r_dihedral_angle_1_deg 6.981 r_mcangle_it 5.402 r_mcangle_other 5.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.168 r_dihedral_angle_4_deg 18.934 r_dihedral_angle_3_deg 18.179 r_lrange_it 9.087 r_lrange_other 9.086 r_scangle_it 7.043 r_scangle_other 7.042 r_dihedral_angle_1_deg 6.981 r_mcangle_it 5.402 r_mcangle_other 5.401 r_scbond_it 4.566 r_scbond_other 4.566 r_mcbond_it 3.676 r_mcbond_other 3.676 r_angle_refined_deg 1.609 r_angle_other_deg 1.341 r_symmetry_xyhbond_nbd_refined 0.251 r_symmetry_nbd_refined 0.25 r_nbd_other 0.248 r_nbd_refined 0.2 r_symmetry_nbd_other 0.198 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.159 r_ncsr_local_group_1 0.097 r_symmetry_nbtor_other 0.083 r_ncsr_local_group_2 0.076 r_chiral_restr 0.073 r_symmetry_xyhbond_nbd_other 0.033 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_bond_refined_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5140 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 137
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing