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Crystal structure of hen egg white lysozyme at 100 Kelvin with Silicone 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 NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.99 38.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.434 α = 90 b = 78.434 β = 90 c = 37.09 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 1.5 21.754 99 0.99 18 1 19064
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 1.5 21.754 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 1.5 21.754 19064 940 99.885 0.179 0.1769 0.1862 0.2124 0.2175 10.008
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 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.128 r_dihedral_angle_3_deg 12.917 r_dihedral_angle_2_deg 11.468 r_dihedral_angle_1_deg 6.52 r_lrange_it 4.779 r_lrange_other 4.652 r_scangle_it 3.196 r_scangle_other 3.194 r_scbond_it 2.166 r_scbond_other 2.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.128 r_dihedral_angle_3_deg 12.917 r_dihedral_angle_2_deg 11.468 r_dihedral_angle_1_deg 6.52 r_lrange_it 4.779 r_lrange_other 4.652 r_scangle_it 3.196 r_scangle_other 3.194 r_scbond_it 2.166 r_scbond_other 2.164 r_angle_refined_deg 1.76 r_mcangle_other 1.554 r_mcangle_it 1.551 r_mcbond_it 1.045 r_mcbond_other 1.043 r_angle_other_deg 0.601 r_xyhbond_nbd_refined 0.317 r_nbd_refined 0.262 r_symmetry_xyhbond_nbd_refined 0.207 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.181 r_nbd_other 0.168 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.077 r_metal_ion_refined 0.065 r_symmetry_nbd_refined 0.053 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 169 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement