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X-ray structure of lysozyme treated with V(V)-lactate complex (structure C)
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 7 293 0.8 M succinic acid pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.88 34.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.399 α = 90 b = 76.399 β = 90 c = 37.012 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 EIGER2 S 16M 2024-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.87313 ESRF ID23-1
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 1.49 54.01 99.9 0.996 7.7 10.5 18528
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 1.49 1.51 0.398
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 1.524 54.006 16004 801 92.653 0.178 0.1755 0.1857 0.2271 0.2299 22.692
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] -0.076 -0.076 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.102 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_1_deg 7.274 r_lrange_it 6.663 r_lrange_other 6.594 r_scangle_it 4.833 r_scangle_other 4.809 r_angle_refined_deg 4.157 r_mcangle_other 3.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.102 r_dihedral_angle_4_deg 18.836 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_1_deg 7.274 r_lrange_it 6.663 r_lrange_other 6.594 r_scangle_it 4.833 r_scangle_other 4.809 r_angle_refined_deg 4.157 r_mcangle_other 3.343 r_mcangle_it 3.335 r_scbond_it 3.14 r_scbond_other 3.025 r_mcbond_it 2.171 r_mcbond_other 2.154 r_angle_other_deg 1.477 r_symmetry_nbd_refined 0.252 r_xyhbond_nbd_refined 0.245 r_nbd_refined 0.228 r_nbd_other 0.196 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.142 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.029 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 110 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing