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Polyoxidovanadate interaction with proteins: crystal structure of lysozyme bound to tetra-vanadate ion (structure 1)
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 buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.96 37.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.05 α = 90 b = 77.05 β = 90 c = 37.84 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 2022-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 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 1.18 38.52 99.9 0.055 0.999 24.1 18 37733
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 1.18 1.2 100 0.872 0.847 2.3 8.8
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 1.183 38.52 36335 1755 96.285 0.172 0.1707 0.1799 0.1961 0.1999 18.152
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] -0.004 -0.004 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 15.321 r_dihedral_angle_1_deg 6.473 r_lrange_it 5.991 r_lrange_other 5.792 r_scangle_it 4.226 r_scangle_other 4.166 r_scbond_it 2.784 r_scbond_other 2.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.526 r_dihedral_angle_4_deg 18.277 r_dihedral_angle_3_deg 15.321 r_dihedral_angle_1_deg 6.473 r_lrange_it 5.991 r_lrange_other 5.792 r_scangle_it 4.226 r_scangle_other 4.166 r_scbond_it 2.784 r_scbond_other 2.723 r_mcangle_other 2.141 r_mcangle_it 2.134 r_angle_refined_deg 2.095 r_angle_other_deg 1.644 r_mcbond_it 1.435 r_mcbond_other 1.423 r_symmetry_nbd_refined 0.253 r_nbd_refined 0.239 r_symmetry_xyhbond_nbd_refined 0.215 r_nbd_other 0.206 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.113 r_metal_ion_refined 0.108 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.054 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 178 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing