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Vibrio cholerae protein FrhA peptide-binding domain and adjacent split domain (S1127-F1439) in complex with peptide AGWTD X-ray crystallography structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6X5W
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 3.14 60.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.273 α = 60.03 b = 118.726 β = 85.62 c = 118.706 γ = 76.7
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 0.98400 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.2 102.74 98.56 0.196 0.212 0.991 1.41 7 182986 25.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 1.061 0.7 0.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 102.72 1.96 108730 1567 98.63 0.227 0.227 0.229 0.2318 0.232 5218
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 14.529 f_angle_d 1.275 f_chiral_restr 0.065 f_plane_restr 0.016 f_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13757 Nucleic Acid Atoms Solvent Atoms 1348 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHENIX phasing Coot model building