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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 4 293 2.0 M sodium formate and 0.1 M Hepes, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.96 37.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.89 α = 90 b = 76.89 β = 90 c = 38.05 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 1.13 54.37 97.3 0.06 0.999 28.4 16.1 42289
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 1.13 1.15 87.9 0.339 0.926 3.4 5
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 1.13 54.369 42156 2091 97.464 0.202 0.1994 0.2016 0.2493 0.2573 16.146
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] -0.855 -0.855 1.709
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.195 r_dihedral_angle_4_deg 18.888 r_dihedral_angle_3_deg 13.348 r_dihedral_angle_1_deg 6.497 r_rigid_bond_restr 6.465 r_lrange_it 3.978 r_scangle_it 3.532 r_scbond_it 3.067 r_mcangle_it 2.322 r_mcbond_it 2.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.195 r_dihedral_angle_4_deg 18.888 r_dihedral_angle_3_deg 13.348 r_dihedral_angle_1_deg 6.497 r_rigid_bond_restr 6.465 r_lrange_it 3.978 r_scangle_it 3.532 r_scbond_it 3.067 r_mcangle_it 2.322 r_mcbond_it 2.014 r_angle_refined_deg 1.883 r_nbtor_refined 0.308 r_symmetry_xyhbond_nbd_refined 0.279 r_metal_ion_refined 0.242 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.202 r_symmetry_nbd_refined 0.184 r_chiral_restr 0.129 r_gen_planes_refined 0.013 r_bond_refined_d 0.012 r_ext_dist_refined_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing