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X-ray structure of lysozyme obtained upon reaction with [VIVO(8-HQ)2] in ethylene glycol
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 4.5 293 20% ethylene glycol, 0.6 M sodium nitrate,
0.1 M sodium acetate at pH 4.5
Crystal Properties Matthews coefficient Solvent content 2 38.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.14 α = 90 b = 78.14 β = 90 c = 37.52 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 2021-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R
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 1.27 55.25 99.9 1 36.5 23.7 31889
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 1.27 1.3 1.629 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-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 1.27 55.236 31030 1532 99.309 0.175 0.1736 0.1804 0.1968 0.2019 23.328
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] -0.022 -0.022 0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 17.161 r_dihedral_angle_3_deg 13.818 r_lrange_it 7.366 r_lrange_other 7.138 r_dihedral_angle_1_deg 6.73 r_scangle_it 5.31 r_scangle_other 5.085 r_scbond_it 3.519 r_scbond_other 3.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 17.161 r_dihedral_angle_3_deg 13.818 r_lrange_it 7.366 r_lrange_other 7.138 r_dihedral_angle_1_deg 6.73 r_scangle_it 5.31 r_scangle_other 5.085 r_scbond_it 3.519 r_scbond_other 3.246 r_mcangle_other 2.647 r_mcangle_it 2.641 r_angle_refined_deg 2.01 r_mcbond_it 1.901 r_mcbond_other 1.871 r_angle_other_deg 1.61 r_nbd_refined 0.234 r_nbd_other 0.217 r_symmetry_nbd_refined 0.204 r_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_other 0.197 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.18 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.09 r_metal_ion_refined 0.068 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 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 147 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing