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X-ray structure of lysozyme obtained upon reaction with [VIVO(malt)2] (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 7.5 293 2.0 M sodium formate
0.1 M hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.97 37.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.08 α = 90 b = 77.08 β = 90 c = 38.09 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 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 1.22 38.54 99.7 0.09 0.999 19.1 18.6 34981
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 1.22 1.24 97.3 1.005 0.747 3.1 12.4
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 1.22 38.54 34951 1728 99.695 0.179 0.1777 0.1867 0.2026 0.1998 17.152
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.437 r_dihedral_angle_4_deg 22.202 r_dihedral_angle_3_deg 13.275 r_dihedral_angle_1_deg 6.17 r_lrange_other 5.701 r_lrange_it 5.532 r_scangle_other 3.789 r_scangle_it 3.642 r_scbond_other 2.413 r_scbond_it 2.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.437 r_dihedral_angle_4_deg 22.202 r_dihedral_angle_3_deg 13.275 r_dihedral_angle_1_deg 6.17 r_lrange_other 5.701 r_lrange_it 5.532 r_scangle_other 3.789 r_scangle_it 3.642 r_scbond_other 2.413 r_scbond_it 2.344 r_mcangle_other 2.251 r_mcangle_it 2.239 r_angle_refined_deg 1.813 r_angle_other_deg 1.603 r_mcbond_it 1.505 r_mcbond_other 1.469 r_nbd_refined 0.24 r_symmetry_nbd_other 0.194 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.165 r_symmetry_nbd_refined 0.148 r_metal_ion_refined 0.123 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.019 r_gen_planes_refined 0.016 r_ext_dist_refined_d 0.009 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 141 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing