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The structure of YcfC from Erwinia amylovora as a C-S lyase
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, HANGING DROP 289.15 50 mM sodium formate
Crystal Properties Matthews coefficient Solvent content 3.27 62.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.619 α = 90 b = 152.619 β = 90 c = 73.331 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 2022-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.09 41.8 93.38 0.04886 14.67 20 50350
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.142 0.844
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 THROUGHOUT 2.09 41.8 48272 1913 93.39 0.1847 0.197 0.2299 0.2342 RANDOM 48.375
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] 1.87 1.87 -3.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.473 r_long_range_B_refined 12.919 r_long_range_B_other 12.881 r_dihedral_angle_2_deg 11.4 r_scangle_other 10.772 r_dihedral_angle_1_deg 7.929 r_scbond_other 7.84 r_scbond_it 7.836 r_mcangle_it 7.771 r_mcangle_other 7.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.473 r_long_range_B_refined 12.919 r_long_range_B_other 12.881 r_dihedral_angle_2_deg 11.4 r_scangle_other 10.772 r_dihedral_angle_1_deg 7.929 r_scbond_other 7.84 r_scbond_it 7.836 r_mcangle_it 7.771 r_mcangle_other 7.769 r_mcbond_it 6.094 r_mcbond_other 6.091 r_angle_refined_deg 2.469 r_angle_other_deg 0.871 r_chiral_restr 0.126 r_bond_refined_d 0.017 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4523 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing