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X-ray structure of lysozyme treated with V(V)-lactate complex (structure A)
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 1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.96 37.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.85 α = 90 b = 77.85 β = 90 c = 37.09 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 2023-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.2 55.05 100 0.999 19.7 12.2 36597
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 1.2 1.22 0.856
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 1.2 55.048 36198 1826 99.97 0.176 0.1745 0.1821 0.2014 0.2088 21.4
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] 0.57 0.57 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.469 r_dihedral_angle_4_deg 23.412 r_lrange_other 17.466 r_lrange_it 17.365 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_1_deg 6.608 r_scangle_it 4.413 r_scangle_other 4.406 r_scbond_it 2.912 r_scbond_other 2.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.469 r_dihedral_angle_4_deg 23.412 r_lrange_other 17.466 r_lrange_it 17.365 r_dihedral_angle_3_deg 16.215 r_dihedral_angle_1_deg 6.608 r_scangle_it 4.413 r_scangle_other 4.406 r_scbond_it 2.912 r_scbond_other 2.865 r_mcangle_it 2.29 r_mcangle_other 2.289 r_angle_refined_deg 1.908 r_mcbond_it 1.652 r_mcbond_other 1.603 r_angle_other_deg 1.58 r_symmetry_nbd_refined 0.306 r_nbd_other 0.291 r_nbd_refined 0.27 r_symmetry_xyhbond_nbd_other 0.259 r_xyhbond_nbd_refined 0.235 r_symmetry_nbd_other 0.215 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.157 r_xyhbond_nbd_other 0.133 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.073 r_bond_refined_d 0.014 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 158 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing