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Crystal structure of VcSiaP in complex with a VHH antibody (VHH_VcP#2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MAG experimental model PDB 5OVW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293.15 Imidazole, MES monohydrate, pH 6.5, PEG 550 MME, PEG 20000, 1,6-Hexanediol, 1-Butanol, 1,2-Propanediol, 2-Propanol, 1,4-Butanediol, 1,3-Propanediol
Crystal Properties Matthews coefficient Solvent content 2.34 47.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.296 α = 90 b = 50.34 β = 114.88 c = 133.994 γ = 90
Symmetry Space Group C 1 2 1
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 2M 2021-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.05 46.38 99.54 0.09801 0.992 7.48 2 57531 26.91
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 2.05 2.13 0.7936 0.436
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 2.05 46.38 1.34 57531 1997 99.55 0.1973 0.1952 0.1955 0.2572 0.2557 34.38
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 9.0488 f_angle_d 1.2024 f_chiral_restr 0.0589 f_bond_d 0.013 f_plane_restr 0.0109
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6647 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 46
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing