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Crystal structure of hen egg white lysozyme at 100 Kelvin with Mineral Oil
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 38.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.431 α = 90 b = 78.431 β = 90 c = 37.126 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 1.498 25.496 99.687 0.99 18 1 19120
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 1.498 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 1.498 25.496 19120 943 99.687 0.175 0.1736 0.2016 0.2055 0.2336 9.345
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] -0.001 -0.001 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.07 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_2_deg 9.812 r_dihedral_angle_1_deg 6.458 r_lrange_it 5.6 r_lrange_other 5.323 r_scangle_it 2.897 r_scangle_other 2.895 r_scbond_it 2.111 r_scbond_other 2.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.07 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_2_deg 9.812 r_dihedral_angle_1_deg 6.458 r_lrange_it 5.6 r_lrange_other 5.323 r_scangle_it 2.897 r_scangle_other 2.895 r_scbond_it 2.111 r_scbond_other 2.109 r_angle_refined_deg 1.819 r_mcangle_other 1.36 r_mcangle_it 1.355 r_mcbond_it 0.895 r_mcbond_other 0.893 r_angle_other_deg 0.634 r_xyhbond_nbd_refined 0.309 r_nbd_refined 0.268 r_symmetry_xyhbond_nbd_refined 0.25 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.182 r_nbd_other 0.14 r_chiral_restr 0.096 r_symmetry_nbd_refined 0.087 r_symmetry_nbtor_other 0.077 r_metal_ion_refined 0.062 r_gen_planes_refined 0.011 r_bond_refined_d 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 132 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement