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Crystal structure of farnesylated and methylated kras4b in complex with PDE-delta (crystal form II - with ordered 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 HEPES:NaOH pH 7.5 and 2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.14 α = 90 b = 70.495 β = 90 c = 84.684 γ = 90
Symmetry Space Group P 21 21 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 PILATUS 6M-F 2015-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979200 APS 24-ID-C
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 1.9 50.01 99.8 0.062 0.999 19.56 7.2 27609 -3 37.255
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 1.9 1.96 99 0.82 0.797 3.3 7.2
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 (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 THROUGHOUT 4OBE, 3T5G 1.9 50.01 26207 1819 99.77 0.22596 0.22326 0.2273 0.26575 0.2647 RANDOM 37.483
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] -0.5 -1.26 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.011 r_dihedral_angle_3_deg 14.394 r_dihedral_angle_4_deg 14.298 r_dihedral_angle_1_deg 5.654 r_long_range_B_refined 4.809 r_long_range_B_other 4.809 r_scangle_other 3.318 r_mcangle_it 2.666 r_mcangle_other 2.666 r_scbond_it 1.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.011 r_dihedral_angle_3_deg 14.394 r_dihedral_angle_4_deg 14.298 r_dihedral_angle_1_deg 5.654 r_long_range_B_refined 4.809 r_long_range_B_other 4.809 r_scangle_other 3.318 r_mcangle_it 2.666 r_mcangle_other 2.666 r_scbond_it 1.981 r_scbond_other 1.981 r_mcbond_it 1.656 r_mcbond_other 1.653 r_angle_refined_deg 1.302 r_angle_other_deg 0.854 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2672 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction Coot model building