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Crystal structure of hen egg white lysozyme at 325 Kelvin
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 2.09 41.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.612 α = 90 b = 79.612 β = 90 c = 37.718 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 325 CMOS BRUKER PHOTON 100 2020-11-30 L LAUE
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 35.63 98.05 0.788 5.29 1.88 19859
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 35.63 0.788
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3A8Z 1.5 35.629 19859 1027 98.055 0.204 0.2021 0.2018 0.2427 0.2421 25.765
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] -0.005 -0.005 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.188 r_dihedral_angle_4_deg 24.487 r_dihedral_angle_3_deg 12.681 r_lrange_it 7.568 r_lrange_other 7.564 r_dihedral_angle_1_deg 6.706 r_scangle_it 5.699 r_scangle_other 5.696 r_scbond_it 3.587 r_scbond_other 3.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.188 r_dihedral_angle_4_deg 24.487 r_dihedral_angle_3_deg 12.681 r_lrange_it 7.568 r_lrange_other 7.564 r_dihedral_angle_1_deg 6.706 r_scangle_it 5.699 r_scangle_other 5.696 r_scbond_it 3.587 r_scbond_other 3.583 r_mcangle_other 3.06 r_mcangle_it 3.05 r_mcbond_it 2.114 r_mcbond_other 2.088 r_angle_refined_deg 1.631 r_angle_other_deg 1.501 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.231 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.167 r_symmetry_xyhbond_nbd_refined 0.128 r_metal_ion_refined 0.12 r_nbd_other 0.117 r_symmetry_nbd_refined 0.103 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_symmetry_xyhbond_nbd_other 0.007 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 30 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction