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Crystal structure of RhoA mutant L69R complexed with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V6U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 5.7 293.15 0.1 M Na acetate (pH 5.7), 0.5 mM Na citrate, 26% PEG4000, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.96 α = 90 b = 64.187 β = 90 c = 83.078 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 CCD RAYONIX MX300-HS 2022-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 1.4 41.54 99.8 0.103 0.112 0.044 0.993 10.9 6.6 34454 9.99
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 1.4 1.42 99.7 0.262 0.285 0.11 0.96 5.7 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 41.54 32623 1756 99.66 0.15448 0.15306 0.1548 0.18173 0.1809 RANDOM 12.222
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] -0.47 0.66 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_dihedral_angle_4_deg 20.655 r_dihedral_angle_3_deg 11.345 r_dihedral_angle_1_deg 6.063 r_long_range_B_refined 4.685 r_long_range_B_other 4.58 r_scangle_other 3.953 r_scbond_other 2.551 r_scbond_it 2.538 r_angle_refined_deg 2.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.178 r_dihedral_angle_4_deg 20.655 r_dihedral_angle_3_deg 11.345 r_dihedral_angle_1_deg 6.063 r_long_range_B_refined 4.685 r_long_range_B_other 4.58 r_scangle_other 3.953 r_scbond_other 2.551 r_scbond_it 2.538 r_angle_refined_deg 2.031 r_mcangle_other 1.999 r_mcangle_it 1.987 r_angle_other_deg 1.499 r_mcbond_it 1.344 r_mcbond_other 1.324 r_chiral_restr 0.106 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 1416 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 29
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling