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Crystal structure of hen egg white lysozyme at 300 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 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.484 α = 90 b = 79.484 β = 90 c = 37.86 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 22.58 99.49 0.736 10.61 1.9 19919
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 22.58 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 22.575 19919 1026 99.486 0.178 0.1764 0.1764 0.203 0.2033 20.662
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 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.484 r_dihedral_angle_4_deg 18.338 r_dihedral_angle_3_deg 13.529 r_lrange_it 7.109 r_lrange_other 7.109 r_dihedral_angle_1_deg 6.646 r_scangle_it 5.523 r_scangle_other 5.52 r_scbond_it 3.51 r_scbond_other 3.507
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.484 r_dihedral_angle_4_deg 18.338 r_dihedral_angle_3_deg 13.529 r_lrange_it 7.109 r_lrange_other 7.109 r_dihedral_angle_1_deg 6.646 r_scangle_it 5.523 r_scangle_other 5.52 r_scbond_it 3.51 r_scbond_other 3.507 r_mcangle_other 2.558 r_mcangle_it 2.55 r_angle_refined_deg 1.833 r_mcbond_it 1.692 r_mcbond_other 1.661 r_angle_other_deg 1.58 r_nbd_refined 0.234 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.174 r_nbd_other 0.121 r_metal_ion_refined 0.115 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.095 r_symmetry_xyhbond_nbd_refined 0.088 r_symmetry_nbtor_other 0.087 r_symmetry_nbd_refined 0.053 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 46 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction