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X-ray structure of lysozyme treated with V(V)-lactate complex (structure B)
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 4 293 20% ethylene glycol, 0.6 M sodium nitrate, 0.1 M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 2.01 38.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.225 α = 90 b = 78.225 β = 90 c = 37.677 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 1.34 55.31 100 0.998 7.8 11.8 25659
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 1.34 1.37 0.378
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 1.355 55.31 23552 1164 90.696 0.177 0.1745 0.1791 0.2166 0.2119 20.786
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] -0.013 -0.013 0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.161 r_dihedral_angle_4_deg 21.696 r_dihedral_angle_3_deg 13.567 r_dihedral_angle_1_deg 6.583 r_lrange_it 6.073 r_lrange_other 5.959 r_scangle_it 4.562 r_scangle_other 4.511 r_scbond_it 3.009 r_scbond_other 2.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.161 r_dihedral_angle_4_deg 21.696 r_dihedral_angle_3_deg 13.567 r_dihedral_angle_1_deg 6.583 r_lrange_it 6.073 r_lrange_other 5.959 r_scangle_it 4.562 r_scangle_other 4.511 r_scbond_it 3.009 r_scbond_other 2.99 r_mcangle_other 2.634 r_mcangle_it 2.63 r_angle_refined_deg 1.92 r_mcbond_it 1.878 r_mcbond_other 1.854 r_angle_other_deg 1.552 r_nbd_refined 0.254 r_nbd_other 0.232 r_xyhbond_nbd_refined 0.23 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.169 r_symmetry_nbd_refined 0.145 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.076 r_metal_ion_refined 0.033 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing