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Crystal structure of hen egg white lysozyme at 225 Kelvin (Duplicate)
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 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.433 α = 90 b = 79.433 β = 90 c = 37.394 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 25.13 99.7 0.796 6.39 1.9 19801
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 25.13 0.796
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 25.13 19801 1017 99.718 0.169 0.1677 0.1675 0.1948 0.1954 14.44
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 -0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.959 r_dihedral_angle_4_deg 20.42 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 6.646 r_lrange_it 4.743 r_lrange_other 4.733 r_scangle_it 3.922 r_scangle_other 3.919 r_scbond_it 2.589 r_scbond_other 2.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.959 r_dihedral_angle_4_deg 20.42 r_dihedral_angle_3_deg 12.442 r_dihedral_angle_1_deg 6.646 r_lrange_it 4.743 r_lrange_other 4.733 r_scangle_it 3.922 r_scangle_other 3.919 r_scbond_it 2.589 r_scbond_other 2.587 r_mcangle_other 1.876 r_mcangle_it 1.875 r_angle_refined_deg 1.723 r_angle_other_deg 1.572 r_mcbond_it 1.235 r_mcbond_other 1.225 r_nbd_refined 0.243 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.101 r_nbd_other 0.096 r_symmetry_xyhbond_nbd_refined 0.096 r_symmetry_nbd_refined 0.094 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.083 r_metal_ion_refined 0.034 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 75 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction