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The DH domain of ARHGEF2 bound to RhoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D0N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 2.6 M sodium formate, 100 mM Tris
Crystal Properties Matthews coefficient Solvent content 2.53 51.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.432 α = 90 b = 71.432 β = 90 c = 196.527 γ = 90
Symmetry Space Group P 43 21 2
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 9M 2022-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 71.43 100 0.072 0.999 10.3 45.8 101036
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 99.9 3.132 0.403 0.7 22.9
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 4D0N 1.4 57.845 100884 2000 99.972 0.131 0.1297 0.1298 0.1751 0.1745 19.506
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] 0.307 0.307 -0.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.665 r_dihedral_angle_3_deg 13.245 r_dihedral_angle_2_deg 8.248 r_scangle_it 6.091 r_scangle_other 6.091 r_scbond_it 5.737 r_scbond_other 5.602 r_dihedral_angle_1_deg 5.566 r_lrange_it 5.512 r_lrange_other 5.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.665 r_dihedral_angle_3_deg 13.245 r_dihedral_angle_2_deg 8.248 r_scangle_it 6.091 r_scangle_other 6.091 r_scbond_it 5.737 r_scbond_other 5.602 r_dihedral_angle_1_deg 5.566 r_lrange_it 5.512 r_lrange_other 5.451 r_rigid_bond_restr 5.15 r_mcangle_it 3.547 r_mcangle_other 3.546 r_mcbond_other 2.91 r_mcbond_it 2.909 r_angle_refined_deg 1.64 r_angle_other_deg 0.609 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.244 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.178 r_nbtor_refined 0.172 r_nbd_other 0.171 r_symmetry_nbd_refined 0.155 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.074 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3427 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing