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ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1137725943
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 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.4 α = 90 b = 71.4 β = 90 c = 197.117 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 2022-10-05 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 1.7 67.13 100 0.367 0.377 0.087 0.997 7.2 18 57254 27.74
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 1.7 1.79 100 10.299 2.358 0.38 18.5 8177
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 1.699 24.81 56578 2794 99 0.2021 0.2007 0.1958 0.2293 0.2288 RANDOM 30.79
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] -2.4406 -2.4406 4.8813
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.74 t_omega_torsion 2.99 t_angle_deg 0.88 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.74 t_omega_torsion 2.99 t_angle_deg 0.88 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3427 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 93
Software Software Software Name Purpose BUSTER refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing