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Crystal structure of hen egg white lysozyme at 100 Kelvin with Mineral Oil (Duplicate)
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 1.99 38.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.48 α = 90 b = 78.48 β = 90 c = 37.111 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 25.5 99 0.99 18 1 19097
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 25.5 19097 941 99.676 0.212 0.2107 0.2198 0.2459 0.2535 9.458
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] -0.009 -0.009 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.13 r_dihedral_angle_3_deg 12.166 r_dihedral_angle_2_deg 8.299 r_dihedral_angle_1_deg 6.65 r_lrange_it 3.601 r_lrange_other 3.558 r_scangle_it 2.972 r_scangle_other 2.97 r_scbond_it 1.947 r_scbond_other 1.946
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.13 r_dihedral_angle_3_deg 12.166 r_dihedral_angle_2_deg 8.299 r_dihedral_angle_1_deg 6.65 r_lrange_it 3.601 r_lrange_other 3.558 r_scangle_it 2.972 r_scangle_other 2.97 r_scbond_it 1.947 r_scbond_other 1.946 r_angle_refined_deg 1.894 r_mcangle_other 1.431 r_mcangle_it 1.427 r_mcbond_it 0.937 r_mcbond_other 0.935 r_angle_other_deg 0.69 r_xyhbond_nbd_refined 0.422 r_nbd_refined 0.26 r_symmetry_xyhbond_nbd_refined 0.238 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.182 r_nbd_other 0.15 r_symmetry_nbd_refined 0.127 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.079 r_metal_ion_refined 0.064 r_bond_refined_d 0.009 r_gen_planes_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 92 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement