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X-ray structure of lysozyme treated with V(V)-lactate complex (structure D)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.0 M sodium formate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.88 34.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.405 α = 90 b = 76.405 β = 90 c = 36.976 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 EIGER2 S 16M 2024-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87313 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.23 54.03 95.3 0.998 12.6 8.9 30853
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 1.23 1.25 0.331
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-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.23 54.026 29851 1468 92.269 0.181 0.1797 0.1794 0.2177 0.2172 17.482
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] -0.029 -0.029 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.175 r_dihedral_angle_4_deg 20.536 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_1_deg 6.61 r_lrange_it 5.838 r_lrange_other 5.624 r_angle_refined_deg 4.171 r_scangle_it 4.144 r_scangle_other 4.139 r_scbond_it 2.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.175 r_dihedral_angle_4_deg 20.536 r_dihedral_angle_3_deg 14.648 r_dihedral_angle_1_deg 6.61 r_lrange_it 5.838 r_lrange_other 5.624 r_angle_refined_deg 4.171 r_scangle_it 4.144 r_scangle_other 4.139 r_scbond_it 2.653 r_scbond_other 2.642 r_mcangle_other 2.471 r_mcangle_it 2.469 r_mcbond_it 1.705 r_mcbond_other 1.702 r_angle_other_deg 1.646 r_metal_ion_refined 0.277 r_symmetry_nbd_refined 0.266 r_nbd_refined 0.243 r_nbd_other 0.239 r_symmetry_xyhbond_nbd_refined 0.225 r_xyhbond_nbd_refined 0.222 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.176 r_chiral_restr 0.107 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.071 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing