☰ Navigation Tabs
Crystal structure of hen egg white lysozyme at 100 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 2.02 39.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.835 α = 90 b = 78.835 β = 90 c = 37.241 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 100 CMOS BRUKER PHOTON 100 2020-10-05 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 25.62 99.68 0.778 6.15 1.9 19440
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 25.62 0.778 6.15
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 25.616 19440 994 99.682 0.181 0.1798 0.189 0.2128 0.2164 11.868
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 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.613 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_1_deg 6.865 r_lrange_it 4.272 r_lrange_other 4.209 r_scangle_it 3.097 r_scangle_other 3.095 r_scbond_it 2.129 r_scbond_other 2.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.613 r_dihedral_angle_4_deg 20.226 r_dihedral_angle_3_deg 13.017 r_dihedral_angle_1_deg 6.865 r_lrange_it 4.272 r_lrange_other 4.209 r_scangle_it 3.097 r_scangle_other 3.095 r_scbond_it 2.129 r_scbond_other 2.127 r_angle_refined_deg 1.87 r_mcangle_it 1.676 r_mcangle_other 1.675 r_angle_other_deg 1.605 r_mcbond_it 1.157 r_mcbond_other 1.107 r_nbd_refined 0.249 r_symmetry_nbd_other 0.2 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.171 r_nbd_other 0.166 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.093 r_symmetry_nbd_refined 0.09 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.084 r_xyhbond_nbd_other 0.044 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 108 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction