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Crystal structure of hen egg white lysozyme at 275 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 2.1 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.79 α = 90 b = 79.79 β = 90 c = 37.785 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 275 CMOS BRUKER PHOTON 100 2020-11-04 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 27.45 96.9 0.822 4.55 1.87 20414
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 27.45 0.822
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 27.449 20414 1056 97.099 0.214 0.2125 0.2188 0.2342 0.2378 18.844
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_2_deg 32.293 r_dihedral_angle_4_deg 24.17 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_1_deg 6.859 r_lrange_it 6.087 r_lrange_other 6.08 r_scangle_it 4.739 r_scangle_other 4.736 r_scbond_it 3.034 r_scbond_other 3.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.293 r_dihedral_angle_4_deg 24.17 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_1_deg 6.859 r_lrange_it 6.087 r_lrange_other 6.08 r_scangle_it 4.739 r_scangle_other 4.736 r_scbond_it 3.034 r_scbond_other 3.031 r_mcangle_other 2.299 r_mcangle_it 2.293 r_angle_refined_deg 1.775 r_mcbond_it 1.591 r_angle_other_deg 1.544 r_mcbond_other 1.519 r_nbd_refined 0.234 r_nbd_other 0.199 r_symmetry_nbd_other 0.194 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.143 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_refined 0.116 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction