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Crystal structure of hen egg white lysozyme at 100 Kelvin with Lard (Triplicate)
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 38.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.253 α = 90 b = 78.253 β = 90 c = 37.381 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 24.746 99.74 0.9 18 1 19188
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 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 1.497 24.746 19188 947 99.74 0.214 0.2119 0.2215 0.2452 0.2543 10.399
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] -0.004 -0.004 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.501 r_dihedral_angle_3_deg 11.599 r_dihedral_angle_1_deg 6.468 r_dihedral_angle_2_deg 6.334 r_lrange_it 4.02 r_lrange_other 3.906 r_scangle_it 3.121 r_scangle_other 3.119 r_scbond_it 2.005 r_scbond_other 2.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.501 r_dihedral_angle_3_deg 11.599 r_dihedral_angle_1_deg 6.468 r_dihedral_angle_2_deg 6.334 r_lrange_it 4.02 r_lrange_other 3.906 r_scangle_it 3.121 r_scangle_other 3.119 r_scbond_it 2.005 r_scbond_other 2.003 r_angle_refined_deg 1.839 r_mcangle_other 1.597 r_mcangle_it 1.589 r_mcbond_it 1.043 r_mcbond_other 1.041 r_angle_other_deg 0.652 r_xyhbond_nbd_refined 0.373 r_nbd_refined 0.266 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.184 r_nbd_other 0.143 r_chiral_restr 0.094 r_symmetry_nbd_refined 0.088 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.055 r_symmetry_xyhbond_nbd_refined 0.05 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 92 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement