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Crystal structure of hen egg white lysozyme at 100 Kelvin with PEG 400 (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 1.94 36.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.09 α = 90 b = 77.09 β = 90 c = 37.355 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 21.381 99 0.99 18 1 18599
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 21.381 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 21.381 18599 974 99.866 0.191 0.1898 0.1991 0.2121 0.2168 11.637
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] 0.007 0.007 -0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.706 r_dihedral_angle_2_deg 12.432 r_dihedral_angle_3_deg 11.589 r_dihedral_angle_1_deg 6.408 r_lrange_it 4.5 r_lrange_other 4.456 r_scangle_it 3.467 r_scangle_other 3.465 r_scbond_it 2.249 r_scbond_other 2.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.706 r_dihedral_angle_2_deg 12.432 r_dihedral_angle_3_deg 11.589 r_dihedral_angle_1_deg 6.408 r_lrange_it 4.5 r_lrange_other 4.456 r_scangle_it 3.467 r_scangle_other 3.465 r_scbond_it 2.249 r_scbond_other 2.247 r_angle_refined_deg 1.89 r_mcangle_other 1.762 r_mcangle_it 1.756 r_mcbond_it 1.137 r_mcbond_other 1.129 r_angle_other_deg 0.666 r_xyhbond_nbd_refined 0.329 r_nbd_refined 0.253 r_symmetry_nbd_refined 0.212 r_symmetry_xyhbond_nbd_refined 0.199 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.186 r_nbd_other 0.179 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.028 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 105 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement