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Crystal structure of fully modified H-Ras-GppNHp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K8Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1M Ca acetate, 20%(w/v) PEG8000, 0.1M MES (pH6.0)
Crystal Properties Matthews coefficient Solvent content 2.36 47.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.475 α = 90 b = 88.475 β = 90 c = 134.047 γ = 120
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 RAYONIX MX225HE 2016-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 50 100 0.159 0.99 21.6 10.7 7216
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 100 0.49 11
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 3K8Y 2.5 44.68 6878 331 99.89 0.18603 0.1837 0.1899 0.23605 0.2384 RANDOM 22.636
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.671 r_dihedral_angle_4_deg 18.402 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_1_deg 5.992 r_long_range_B_refined 3.34 r_long_range_B_other 3.332 r_scangle_other 1.966 r_mcangle_it 1.808 r_mcangle_other 1.808 r_angle_refined_deg 1.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.671 r_dihedral_angle_4_deg 18.402 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_1_deg 5.992 r_long_range_B_refined 3.34 r_long_range_B_other 3.332 r_scangle_other 1.966 r_mcangle_it 1.808 r_mcangle_other 1.808 r_angle_refined_deg 1.319 r_scbond_other 1.146 r_scbond_it 1.144 r_mcbond_it 1.041 r_mcbond_other 1.04 r_angle_other_deg 0.9 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 1302 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing