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Transition state analogue complex of small G protein and its GAP effector
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WQ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 precipitant: HEPES-Na 100 mM pH = 8.0, PEG3350 22% (w/v), (NH4)2SO4 20 mM, Gd-HCl 100 mM, NaF 20 mM
protein buffer: HRas 0.400 mM, RasGAP 0.400 mM, HEPES-Na 20 mM, NaF 20 mM
drop size: 5 uL, protein:precipitant ratio: 1:1.2
Crystal Properties Matthews coefficient Solvent content 2.26 45.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.832 α = 90 b = 41.558 β = 109.25 c = 89.674 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 PIXEL DECTRIS EIGER2 XE 16M 2021-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.976 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 84.66 54.1 0.176 0.213 0.112 0.981 12.6 3.4 16248
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 0.659 0.821 0.478 0.552 1.7 2.8
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 1WQ1 2.1 84.66 15452 791 54.81 0.20217 0.19802 0.2083 0.27994 0.2899 RANDOM 43.913
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] -0.28 0.04 0.02 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.398 r_long_range_B_refined 7.971 r_long_range_B_other 7.971 r_dihedral_angle_1_deg 7.299 r_dihedral_angle_2_deg 5.693 r_scangle_other 5.381 r_mcangle_other 4.94 r_mcangle_it 4.939 r_scbond_it 3.516 r_scbond_other 3.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.398 r_long_range_B_refined 7.971 r_long_range_B_other 7.971 r_dihedral_angle_1_deg 7.299 r_dihedral_angle_2_deg 5.693 r_scangle_other 5.381 r_mcangle_other 4.94 r_mcangle_it 4.939 r_scbond_it 3.516 r_scbond_other 3.513 r_mcbond_it 3.218 r_mcbond_other 3.205 r_angle_refined_deg 1.437 r_angle_other_deg 0.46 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3914 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling MOLREP phasing xia2 data reduction