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X-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (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
0.1 M sodium acetate pH 4.0
0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.99 38.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.23 α = 90 b = 78.23 β = 90 c = 37.28 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 2021-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.31 55.32 98.9 0.141 0.997 14.3 20 28122
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 1.31 1.33 98.9 1.8 0.755 25.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 193l 1.31 55.317 28065 1403 98.779 0.169 0.1676 0.1761 0.1976 0.2025 18.925
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] 0.037 0.037 -0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.266 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 13.831 r_lrange_it 6.649 r_lrange_other 6.648 r_dihedral_angle_1_deg 6.465 r_scangle_it 4.264 r_scangle_other 4.131 r_scbond_it 2.905 r_scbond_other 2.787
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.266 r_dihedral_angle_4_deg 20.745 r_dihedral_angle_3_deg 13.831 r_lrange_it 6.649 r_lrange_other 6.648 r_dihedral_angle_1_deg 6.465 r_scangle_it 4.264 r_scangle_other 4.131 r_scbond_it 2.905 r_scbond_other 2.787 r_mcangle_other 2.39 r_mcangle_it 2.389 r_angle_refined_deg 1.839 r_mcbond_it 1.67 r_mcbond_other 1.616 r_angle_other_deg 1.58 r_nbd_refined 0.276 r_nbd_other 0.27 r_xyhbond_nbd_refined 0.236 r_symmetry_nbd_refined 0.216 r_symmetry_xyhbond_nbd_refined 0.211 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.174 r_symmetry_metal_ion_refined 0.119 r_metal_ion_refined 0.099 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.089 r_symmetry_xyhbond_nbd_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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 132 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing