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Crystal structure of hen egg white lysozyme at 325 Kelvin (Triplicate)
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 41.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.891 α = 90 b = 79.891 β = 90 c = 37.802 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 2020-11-24 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 22.64 98.29 0.684 5.34 1.82 19827
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 22.64 0.684
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 22.637 19827 1013 98.295 0.215 0.2134 0.221 0.2409 0.2431 26.389
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] 0.003 0.003 -0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.638 r_dihedral_angle_4_deg 24.477 r_dihedral_angle_3_deg 14.62 r_lrange_it 8.027 r_lrange_other 8.02 r_dihedral_angle_1_deg 6.739 r_scangle_it 6.383 r_scangle_other 6.379 r_scbond_it 4.084 r_scbond_other 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.638 r_dihedral_angle_4_deg 24.477 r_dihedral_angle_3_deg 14.62 r_lrange_it 8.027 r_lrange_other 8.02 r_dihedral_angle_1_deg 6.739 r_scangle_it 6.383 r_scangle_other 6.379 r_scbond_it 4.084 r_scbond_other 4.08 r_mcangle_other 3.14 r_mcangle_it 3.134 r_mcbond_it 2.181 r_mcbond_other 2.16 r_angle_refined_deg 1.719 r_angle_other_deg 1.517 r_nbd_refined 0.229 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.18 r_nbtor_refined 0.17 r_nbd_other 0.144 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.092 r_metal_ion_refined 0.086 r_symmetry_nbtor_other 0.082 r_symmetry_nbd_refined 0.056 r_bond_refined_d 0.012 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 27 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction