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Crystal structure of hen egg white lysozyme at 100 Kelvin with Vaseline (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 NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 2 38.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.471 α = 90 b = 78.471 β = 90 c = 37.214 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 21.764 99 0.99 18 1 19213
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 21.764 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 21.764 19213 948 99.647 0.183 0.1807 0.181 0.2179 0.2167 10.929
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_2_deg 20.599 r_dihedral_angle_6_deg 18.019 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 6.473 r_lrange_it 4.543 r_lrange_other 4.401 r_scangle_it 3.079 r_scangle_other 3.077 r_scbond_it 2.445 r_scbond_other 2.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.599 r_dihedral_angle_6_deg 18.019 r_dihedral_angle_3_deg 12.695 r_dihedral_angle_1_deg 6.473 r_lrange_it 4.543 r_lrange_other 4.401 r_scangle_it 3.079 r_scangle_other 3.077 r_scbond_it 2.445 r_scbond_other 2.444 r_angle_refined_deg 1.792 r_mcangle_it 1.514 r_mcangle_other 1.514 r_mcbond_it 1.042 r_mcbond_other 1.031 r_angle_other_deg 0.623 r_xyhbond_nbd_refined 0.3 r_nbd_refined 0.256 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.181 r_nbd_other 0.176 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.046 r_symmetry_nbd_refined 0.033 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement