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Identification of chloride ions in lysozyme at long wavelengths
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 294 100 mM sodium acetate pH 4.6, 1 M NaCl and 25% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.01 38.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.031 α = 90 b = 79.031 β = 90 c = 36.897 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 80 PIXEL DECTRIS PILATUS 12M 2024-07-31 M SINGLE WAVELENGTH 2 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2024-07-31 M SINGLE WAVELENGTH 3 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2024-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 4.1328 Diamond I23 2 SYNCHROTRON DIAMOND BEAMLINE I23 4.5920 Diamond I23 3 SYNCHROTRON DIAMOND BEAMLINE I23 5.1660 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.7 79 76.8 0.07 0.99 62 17.7 2680
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 60.4 0.12 0.99 18.9
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 THROUGHOUT 2.703 55.884 2660 138 76.305 0.189 0.1876 0.1898 0.2171 0.2174 19.357
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] 0.067 0.067 -0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.295 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_2_deg 7.242 r_dihedral_angle_1_deg 6.479 r_lrange_it 6.291 r_scangle_it 3.865 r_scbond_it 2.345 r_mcangle_it 2.186 r_angle_refined_deg 1.76 r_mcbond_it 1.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.295 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_2_deg 7.242 r_dihedral_angle_1_deg 6.479 r_lrange_it 6.291 r_scangle_it 3.865 r_scbond_it 2.345 r_mcangle_it 2.186 r_angle_refined_deg 1.76 r_mcbond_it 1.278 r_nbtor_refined 0.301 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.12 r_metal_ion_refined 0.104 r_symmetry_xyhbond_nbd_refined 0.074 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_ext_dist_refined_b
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing