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Crystal structure of hen egg white lysozyme at 100 Kelvin with Vaseline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 1.2 M NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.95 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.343 α = 90 b = 77.343 β = 90 c = 37.399 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 Bruker PHOTON II 2024-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
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 1.497 24.458 99 0.99 19 1 18783
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 1.497 24.458 0.99
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 1.497 24.458 18783 979 99.703 0.179 0.178 0.1781 0.203 0.203 11.703
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 r_dihedral_angle_6_deg 16.902 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_2_deg 7.138 r_dihedral_angle_1_deg 6.618 r_lrange_it 5.52 r_lrange_other 5.366 r_scangle_it 3.175 r_scangle_other 3.172 r_scbond_it 2.285 r_scbond_other 2.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.902 r_dihedral_angle_3_deg 13.424 r_dihedral_angle_2_deg 7.138 r_dihedral_angle_1_deg 6.618 r_lrange_it 5.52 r_lrange_other 5.366 r_scangle_it 3.175 r_scangle_other 3.172 r_scbond_it 2.285 r_scbond_other 2.283 r_mcangle_other 1.838 r_mcangle_it 1.834 r_angle_refined_deg 1.786 r_mcbond_it 1.25 r_mcbond_other 1.23 r_angle_other_deg 0.642 r_xyhbond_nbd_refined 0.287 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.252 r_nbd_other 0.205 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.182 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.075 r_bond_refined_d 0.01 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 174 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement