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H/D exchanged Hen egg-white lysozyme denatured in acidic conditions and refolded in solution
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6K8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NACL, SODIUM ACETATE-D3, ACETIC ACID-D4
Crystal Properties Matthews coefficient Solvent content 2.07 40.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.182 α = 90 b = 79.182 β = 90 c = 37.906 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 293 IMAGE PLATE RIGAKU RAXIS VII 2018-02-13 M SINGLE WAVELENGTH 2 1 neutron 293 IMAGE PLATE MAATEL IMAGINE 2018-03-19 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54 2 NUCLEAR REACTOR ORNL High Flux Isotope Reactor BEAMLINE CG4D 2.8-4.5 ORNL High Flux Isotope Reactor CG4D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 2 100 99.6 0.027 67.6 14.5 8580 23.63 2 2 100 91 0.166 6.5 8.5 7546 23.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 0.08 2 2 2.11 0.268
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 2 39.59 1.37 8542 418 99.62 0.1425 0.1403 0.144 0.1829 0.1472 22.41 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 55.99 7546 91 0.2328 0.2656
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.2902 f_angle_d 0.8166 f_chiral_restr 0.0542 f_bond_d 0.0058 f_plane_restr 0.0043
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 997 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing