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Crystal structure of hen egg white lysozyme at 100 Kelvin with Glycerol 30% (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 1.96 37.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.783 α = 90 b = 77.783 β = 90 c = 37.115 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 22.096 99.709 0.99 18 1 18832
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 22.096 18832 979 99.709 0.177 0.1752 0.185 0.2067 0.2151 12.266
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] -0.002 -0.002 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.503 r_dihedral_angle_6_deg 17.289 r_dihedral_angle_3_deg 13.846 r_dihedral_angle_1_deg 6.621 r_lrange_it 4.595 r_lrange_other 4.433 r_scangle_it 3.134 r_scangle_other 3.132 r_scbond_it 2.042 r_scbond_other 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 19.503 r_dihedral_angle_6_deg 17.289 r_dihedral_angle_3_deg 13.846 r_dihedral_angle_1_deg 6.621 r_lrange_it 4.595 r_lrange_other 4.433 r_scangle_it 3.134 r_scangle_other 3.132 r_scbond_it 2.042 r_scbond_other 2.04 r_mcangle_it 1.787 r_mcangle_other 1.787 r_angle_refined_deg 1.724 r_mcbond_it 1.186 r_mcbond_other 1.185 r_angle_other_deg 0.597 r_xyhbond_nbd_refined 0.317 r_nbd_refined 0.249 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.184 r_nbd_other 0.167 r_symmetry_xyhbond_nbd_refined 0.167 r_metal_ion_refined 0.099 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_other 0.04 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 129 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement