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Crystal structure of hen egg white lysozyme at 200 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 2.02 38.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.903 α = 90 b = 78.903 β = 90 c = 37.112 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 200 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 22.31 99.93 0.736 15.06 1.91 19331
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 22.31 0.736
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 22.309 19331 988 99.928 0.17 0.1684 0.1775 0.1948 0.202 10.001
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 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.344 r_dihedral_angle_4_deg 19.589 r_dihedral_angle_3_deg 11.834 r_dihedral_angle_1_deg 6.527 r_lrange_it 4.101 r_lrange_other 3.96 r_scangle_it 3.024 r_scangle_other 3.022 r_scbond_it 2.038 r_scbond_other 2.037
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.344 r_dihedral_angle_4_deg 19.589 r_dihedral_angle_3_deg 11.834 r_dihedral_angle_1_deg 6.527 r_lrange_it 4.101 r_lrange_other 3.96 r_scangle_it 3.024 r_scangle_other 3.022 r_scbond_it 2.038 r_scbond_other 2.037 r_angle_refined_deg 1.89 r_angle_other_deg 1.627 r_mcangle_other 1.251 r_mcangle_it 1.249 r_mcbond_it 0.818 r_mcbond_other 0.806 r_nbd_refined 0.246 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.175 r_nbd_other 0.155 r_symmetry_xyhbond_nbd_refined 0.117 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.088 r_metal_ion_refined 0.07 r_symmetry_nbd_refined 0.04 r_bond_refined_d 0.013 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 142 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction