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Vibrio cholerae protein FrhA peptide-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGYTD X-ray crystallography structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 9 293 0.16 M calcium acetate, 0.08 M sodium cacodylate, and 24.4% (w/v) PEG 8000.
Ethylene glycol was used as a cryoprotectant.
Crystal Properties Matthews coefficient Solvent content 3.15 60.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.394 α = 60.05 b = 118.717 β = 76.45 c = 118.728 γ = 81.42
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD RAYONIX MX300HE 2020-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 2.2 59.64 98.1 0.212 0.252 0.135 0.904 3.4 3.4 140116
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 2.2 2.24 95.7 0.593 0.718 0.396 0.159 0.8 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 59.18 1.96 95982 1361 98.28 0.248 0.2479 0.2509 0.2518 0.2581
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.5 f_angle_d 1.704 f_chiral_restr 0.076 f_plane_restr 0.026 f_bond_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13910 Nucleic Acid Atoms Solvent Atoms 1712 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction DIALS data scaling PHENIX phasing Coot model building