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Crystal structure of hen egg white lysozyme at 300 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 2.14 42.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.422 α = 90 b = 80.422 β = 90 c = 37.997 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 300 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 22.78 98.05 0.662 6.91 1.81 20655
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 22.78 0.662
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A8Z 1.5 22.776 20655 1073 98.054 0.2 0.1988 0.2276 0.1761 21.998
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 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.897 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 14.322 r_lrange_it 6.964 r_lrange_other 6.962 r_dihedral_angle_1_deg 6.598 r_scangle_it 5.441 r_scangle_other 5.438 r_scbond_it 3.494 r_scbond_other 3.491
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.897 r_dihedral_angle_4_deg 19.483 r_dihedral_angle_3_deg 14.322 r_lrange_it 6.964 r_lrange_other 6.962 r_dihedral_angle_1_deg 6.598 r_scangle_it 5.441 r_scangle_other 5.438 r_scbond_it 3.494 r_scbond_other 3.491 r_mcangle_other 2.889 r_mcangle_it 2.87 r_mcbond_it 1.962 r_mcbond_other 1.908 r_angle_refined_deg 1.807 r_angle_other_deg 1.498 r_nbd_refined 0.231 r_symmetry_nbd_other 0.192 r_nbtor_refined 0.163 r_symmetry_xyhbond_nbd_refined 0.115 r_xyhbond_nbd_refined 0.105 r_nbd_other 0.093 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.082 r_symmetry_nbd_refined 0.069 r_metal_ion_refined 0.054 r_bond_refined_d 0.011 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 41 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction