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Crystal structure of hen egg white lysozyme at 100 Kelvin with Lard
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 sodium chloride, 100 mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2 38.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.448 α = 90 b = 78.448 β = 90 c = 37.228 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 1.499 24.807 99 0.99 19 1 19148
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 1.499 10 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 1.499 24.807 19148 943 99.719 0.217 0.2158 0.2253 0.247 0.2495 11.397
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] -0.011 -0.011 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.783 r_dihedral_angle_3_deg 11.515 r_dihedral_angle_2_deg 8.673 r_dihedral_angle_1_deg 6.64 r_lrange_other 4.194 r_lrange_it 4.186 r_scangle_it 3.329 r_scangle_other 3.327 r_scbond_it 2.125 r_scbond_other 2.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.783 r_dihedral_angle_3_deg 11.515 r_dihedral_angle_2_deg 8.673 r_dihedral_angle_1_deg 6.64 r_lrange_other 4.194 r_lrange_it 4.186 r_scangle_it 3.329 r_scangle_other 3.327 r_scbond_it 2.125 r_scbond_other 2.123 r_angle_refined_deg 1.845 r_mcangle_other 1.781 r_mcangle_it 1.777 r_mcbond_it 1.146 r_mcbond_other 1.139 r_angle_other_deg 0.643 r_xyhbond_nbd_refined 0.422 r_nbd_refined 0.263 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.184 r_nbd_other 0.144 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.077 r_metal_ion_refined 0.073 r_symmetry_nbd_refined 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_refined 0.009 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 89 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement