☰ Navigation Tabs
X-ray structure of lysozyme obtained upon reaction with [VIVO(empp)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 1.1 M sodium chloride, 0.1 M sodium acetate pH 4.0
Crystal Properties Matthews coefficient Solvent content 1.97 37.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.06 α = 90 b = 78.06 β = 90 c = 37.01 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 2022-07-28 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 1.08 55.4 100 1 33.2 20 50384
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 1.08 1.1 0.744
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 1.08 55.258 45671 2314 92.194 0.15 0.1476 0.1528 0.1895 0.1988 20.124
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] 1.684 1.684 -3.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.163 r_dihedral_angle_4_deg 17.774 r_rigid_bond_restr 14.495 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 6.421 r_scangle_it 5.64 r_scangle_other 5.606 r_scbond_other 5.374 r_scbond_it 5.359 r_lrange_it 4.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.163 r_dihedral_angle_4_deg 17.774 r_rigid_bond_restr 14.495 r_dihedral_angle_3_deg 12.752 r_dihedral_angle_1_deg 6.421 r_scangle_it 5.64 r_scangle_other 5.606 r_scbond_other 5.374 r_scbond_it 5.359 r_lrange_it 4.65 r_lrange_other 4.27 r_angle_refined_deg 2.967 r_mcangle_other 2.436 r_mcangle_it 2.422 r_mcbond_it 2.361 r_mcbond_other 2.322 r_angle_other_deg 1.71 r_nbd_refined 0.343 r_symmetry_nbd_other 0.257 r_nbd_other 0.257 r_xyhbond_nbd_refined 0.225 r_symmetry_nbd_refined 0.204 r_symmetry_xyhbond_nbd_other 0.201 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.167 r_chiral_restr 0.141 r_symmetry_nbtor_other 0.089 r_metal_ion_refined 0.042 r_bond_refined_d 0.022 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing