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ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1203730981
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 2.47 50.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.72 α = 90 b = 70.72 β = 90 c = 196.03 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 2.14 70.72 100 0.507 0.517 0.101 0.996 5.4 26 28461
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.2 99.9 15.137 2.882 0.387 27.3 2047
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 66.52 21847 1168 99.97 0.2013 0.1979 0.2024 0.2657 0.266 RANDOM 62.977
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] 3.18 3.18 -6.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.243 r_mcangle_it 7.03 r_dihedral_angle_2_deg 6.56 r_dihedral_angle_1_deg 6.185 r_mcbond_it 4.881 r_mcbond_other 4.881 r_angle_refined_deg 1.35 r_angle_other_deg 0.454 r_chiral_restr 0.061 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.243 r_mcangle_it 7.03 r_dihedral_angle_2_deg 6.56 r_dihedral_angle_1_deg 6.185 r_mcbond_it 4.881 r_mcbond_other 4.881 r_angle_refined_deg 1.35 r_angle_other_deg 0.454 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3410 Nucleic Acid Atoms Solvent Atoms 59 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing