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Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FOE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 9.5 293 25 mM CHES pH 9.5, 25% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.063 α = 83.37 b = 54.16 β = 76.34 c = 94.004 γ = 62.52
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 EIGER X 16M 2019-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.98 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 50 81.7 0.038 0.053 0.038 10.4 1.6 92107
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 1.6 1.63 80.2 0.731 1.033 0.731 0.295 1.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1FOE 1.6 48.05 87425 4663 81.52 0.1828 0.181 0.1899 0.2182 0.2247 RANDOM 45.588
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] 0.14 0.29 -0.22 -0.37 -0.05 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.414 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 6.023 r_angle_refined_deg 1.808 r_angle_other_deg 1.517 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.414 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 6.023 r_angle_refined_deg 1.808 r_angle_other_deg 1.517 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6266 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing