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Crystal structure of full-length farnesylated and methylated KRAS4b in complex with PDE-delta (crystal form I - with partially disordered hypervariable region)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OBE 4OBE, 3T5G experimental model PDB 3T5G 4OBE, 3T5G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M citrate pH 5.0 and 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.52 51.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.386 α = 90 b = 70.651 β = 92.4 c = 94.307 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.979180 APS 24-ID-E
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 1.99 50 99.2 0.052 0.999 20.51 6.2 52173 -3 36.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.05 98.3 0.798 0.776 2.62 5.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4OBE, 3T5G 2 48.695 1.35 51556 5200 99.24 0.2054 0.2007 0.203 0.2476 0.2428 Random
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 f_dihedral_angle_d 18.285 f_angle_d 1.012 f_chiral_restr 0.053 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5117 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling XDS data reduction Coot model building PDB_EXTRACT data extraction