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Perdeuterated hen egg-white lysozyme at 100 K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YEO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.5 291 sodium nitrate, sodium acetate pD 4.5
Crystal Properties Matthews coefficient Solvent content 1.7 27.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.67 α = 89.439 b = 30.97 β = 72.818 c = 33.74 γ = 67.503
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 X 16M 2019-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.7999 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1 32.01 97.71 0.0803 0.0876 0.0344 0.992 15.07 6.7 49991 8.81
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1 1.036 95.5 0.262 0.284 0.109 0.979 6.92
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4yeo 1 32.01 2.07 49982 2400 97.71 0.121 0.1205 0.1207 0.1341 0.1344 11.84
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 13.4583 f_angle_d 1.6163 f_chiral_restr 0.1038 f_plane_restr 0.0146 f_bond_d 0.0127
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing Coot model building