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Crystal structure of hen egg white lysozyme at 225 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 2.03 39.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.178 α = 90 b = 79.178 β = 90 c = 37.136 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 225 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 22.36 99.6 0.787 4.48 1.9 19544
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 22.36 0.787
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 22.36 19544 998 99.597 0.193 0.1914 0.1984 0.2258 0.2326 15.866
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 33.963 r_dihedral_angle_4_deg 20.667 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 6.789 r_lrange_it 4.183 r_lrange_other 4.175 r_scangle_it 3.344 r_scangle_other 3.342 r_scbond_it 2.168 r_scbond_other 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.963 r_dihedral_angle_4_deg 20.667 r_dihedral_angle_3_deg 13.159 r_dihedral_angle_1_deg 6.789 r_lrange_it 4.183 r_lrange_other 4.175 r_scangle_it 3.344 r_scangle_other 3.342 r_scbond_it 2.168 r_scbond_other 2.165 r_mcangle_it 1.883 r_mcangle_other 1.882 r_angle_refined_deg 1.718 r_angle_other_deg 1.53 r_mcbond_it 1.307 r_mcbond_other 1.307 r_nbd_refined 0.234 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.17 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.137 r_symmetry_nbd_refined 0.123 r_chiral_restr 0.089 r_symmetry_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.07 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 69 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction