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H-Ras Q61L in complex with GppNHp (state 1) after structural transition by humidity control
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 PEG400, SODIUM ACETATE, CALCIUM
ACETATE
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.844 α = 90 b = 91.844 β = 90 c = 121.413 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 ADSC QUANTUM 315r 2016-04-26 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 Merge I (Observed) 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 1.976 45.93 99.9 0.122 37.5 10.6 14025
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.976 2 0.462
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 3k8y 1.976 45.93 14025 1408 99.915 0.193 0.1895 0.1936 0.221 0.2217 22.144
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] -0.003 -0.001 -0.003 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.367 r_dihedral_angle_4_deg 20.432 r_dihedral_angle_3_deg 12.558 r_dihedral_angle_1_deg 6.203 r_lrange_it 4.407 r_lrange_other 4.27 r_scangle_other 2.612 r_scangle_it 2.609 r_mcangle_it 2.118 r_mcangle_other 2.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.367 r_dihedral_angle_4_deg 20.432 r_dihedral_angle_3_deg 12.558 r_dihedral_angle_1_deg 6.203 r_lrange_it 4.407 r_lrange_other 4.27 r_scangle_other 2.612 r_scangle_it 2.609 r_mcangle_it 2.118 r_mcangle_other 2.117 r_scbond_other 1.611 r_scbond_it 1.609 r_angle_refined_deg 1.376 r_mcbond_it 1.296 r_mcbond_other 1.294 r_angle_other_deg 1.275 r_symmetry_nbd_refined 0.312 r_symmetry_metal_ion_refined 0.214 r_metal_ion_refined 0.208 r_nbd_refined 0.206 r_symmetry_nbd_other 0.181 r_nbd_other 0.18 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.131 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1258 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing