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Crystal structure of carbon-sulfur lyase FnaPatB1 from Fusobacterium nucleatum subspecies animalis in complex with allyl-cysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QP2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 40 % PEG 300, 0.2 M magnesium chloride in 0.1 M sodium cacodylate-HCl pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.01 59.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.049 α = 90 b = 106.049 β = 90 c = 204.062 γ = 90
Symmetry Space Group P 43 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 PILATUS 6M 2021-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM07 0.979511 ESRF BM07
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 2.6 47.43 100 0.142 0.148 1 15 13.1 36686 59.73
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 2.6 2.72 100 1.8 0.71 1.6 13.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6QP2 2.6 19.29 1.34 36489 1860 99.96 0.2173 0.2145 0.215 0.2678 0.2681 58.01
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 26.7039 f_angle_d 1.0853 f_chiral_restr 0.0579 f_bond_d 0.0087 f_plane_restr 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6355 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX refinement PHENIX refinement Aimless data scaling PHASER phasing XDS data reduction