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Crystal structure of hen egg white lysozyme at 300 Kelvin with Apiezon T (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 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.134 α = 90 b = 79.134 β = 90 c = 38.219 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 PIXEL Bruker PHOTON II 2024-07-01 M SINGLE WAVELENGTH
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 1.472 27.489 99 0.99 18 1 20433
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 1.472 1.5 0.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.472 27.489 20433 1003 96.724 0.171 0.1694 0.1694 0.1984 0.1988 19.48
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_6_deg 14.252 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_2_deg 10.032 r_lrange_it 7.605 r_lrange_other 7.603 r_scangle_it 6.444 r_scangle_other 6.44 r_dihedral_angle_1_deg 6.193 r_scbond_it 4.095 r_scbond_other 4.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.252 r_dihedral_angle_3_deg 11.066 r_dihedral_angle_2_deg 10.032 r_lrange_it 7.605 r_lrange_other 7.603 r_scangle_it 6.444 r_scangle_other 6.44 r_dihedral_angle_1_deg 6.193 r_scbond_it 4.095 r_scbond_other 4.091 r_mcangle_other 2.872 r_mcangle_it 2.85 r_angle_refined_deg 2.003 r_mcbond_it 1.9 r_mcbond_other 1.898 r_angle_other_deg 0.702 r_xyhbond_nbd_refined 0.46 r_nbd_refined 0.254 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.182 r_nbd_other 0.142 r_chiral_restr 0.118 r_symmetry_nbd_refined 0.101 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.044 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_symmetry_xyhbond_nbd_refined 0.007 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 74 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing