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Crystal structure of Bdellovibrio bacteriovorus Bd2439 fibre C-terminal domains with ethylene glycol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.1 M Sodium chloride 0.1 M Sodium formate 0.1 M Bis-Tris propane 8.5
6.25 % w/v PEG 3350 6.25%w/v PEG 4000 6.25%w/v PEG 2000 6.25%w/v PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 1.95 36.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.368 α = 90 b = 161.278 β = 90 c = 52.067 γ = 90
Symmetry Space Group P 21 21 2
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 9M 2022-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.979 ESRF ID30B
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 1.53 84.37 96.9 0.062 0.073 0.037 0.998 11.2 3.3 104740
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 1.53 1.55 79.3 0.653 0.842 0.526 0.638 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.53 45.34 1.34 104674 5230 96.5 0.1653 0.1643 0.1851 0.1865
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 7.287 f_angle_d 0.863 f_chiral_restr 0.061 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5710 Nucleic Acid Atoms Solvent Atoms 937 Heterogen Atoms 28
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing