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Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X1G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7 293 2.4 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.93 58.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.533 α = 90 b = 110.533 β = 90 c = 251.24 γ = 120
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 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 2.9 50 100 0.116 0.123 0.042 4.6 8.4 37764
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 2.9 2.95 100 1.948 2.107 0.793 0.288 6.8
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 6X1G 2.91 47.86 35812 1904 99.64 0.1683 0.1663 0.1677 0.2082 0.2041 RANDOM 154.331
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] -19.85 -19.85 39.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.149 r_dihedral_angle_4_deg 22.285 r_dihedral_angle_3_deg 17.861 r_dihedral_angle_1_deg 5.731 r_angle_other_deg 2.323 r_angle_refined_deg 1.657 r_chiral_restr 0.076 r_bond_other_d 0.035 r_gen_planes_other 0.015 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.149 r_dihedral_angle_4_deg 22.285 r_dihedral_angle_3_deg 17.861 r_dihedral_angle_1_deg 5.731 r_angle_other_deg 2.323 r_angle_refined_deg 1.657 r_chiral_restr 0.076 r_bond_other_d 0.035 r_gen_planes_other 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10288 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 1
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing