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H-Ras Q61H 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 5 293 PEG400, SODIUM ACETATE, CALCIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.68 54.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.769 α = 90 b = 91.769 β = 90 c = 121.268 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 2018-01-21 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 1.54 50 99.8 0.043 68.4 10.4 29269
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 1.54 1.57 0.333 9.3
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 1.54 23.208 29199 1406 99.761 0.193 0.1922 0.2019 0.2023 0.2135 17.994
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] -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.456 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 6.128 r_lrange_it 3.522 r_lrange_other 3.405 r_scangle_other 1.604 r_scangle_it 1.602 r_mcangle_it 1.493 r_mcangle_other 1.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.456 r_dihedral_angle_4_deg 19.473 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 6.128 r_lrange_it 3.522 r_lrange_other 3.405 r_scangle_other 1.604 r_scangle_it 1.602 r_mcangle_it 1.493 r_mcangle_other 1.493 r_angle_refined_deg 1.293 r_angle_other_deg 1.25 r_scbond_it 0.985 r_scbond_other 0.984 r_mcbond_it 0.85 r_mcbond_other 0.841 r_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.183 r_metal_ion_refined 0.181 r_symmetry_nbd_other 0.178 r_symmetry_nbd_refined 0.155 r_nbtor_refined 0.147 r_xyhbond_nbd_refined 0.147 r_nbd_other 0.139 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.054 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1234 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing