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ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z57899718
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BNT 8BNT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 100 mM Tris, 2.6M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.226 α = 90 b = 71.226 β = 90 c = 196.058 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 PILATUS 6M 2023-03-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
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 2.3 71.27 100 0.636 0.666 0.143 0.992 6.1 21 23427
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 2.3 2.38 100 5.282 5.498 1.18 0.629 21.4 2237
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 FOURIER SYNTHESIS THROUGHOUT 8BNT 2.3 66.94 22169 1158 99.89 0.1928 0.1898 0.1989 0.249 0.2511 RANDOM 36.521
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] 1.15 1.15 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.161 r_dihedral_angle_2_deg 7.653 r_dihedral_angle_1_deg 6.71 r_mcangle_it 5.408 r_mcbond_it 3.475 r_mcbond_other 3.475 r_angle_refined_deg 1.566 r_angle_other_deg 0.516 r_chiral_restr 0.072 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.161 r_dihedral_angle_2_deg 7.653 r_dihedral_angle_1_deg 6.71 r_mcangle_it 5.408 r_mcbond_it 3.475 r_mcbond_other 3.475 r_angle_refined_deg 1.566 r_angle_other_deg 0.516 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3340 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing