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Crystal structure of hen egg white lysozyme at 300 Kelvin with Apiezon N (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 41.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.233 α = 90 b = 79.233 β = 90 c = 38.105 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 1.499 25.056 99 0.99 18 1 19730
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 1.4999 25.056 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 1.499 25.056 19730 955 98.419 0.265 0.2627 0.2693 0.3224 0.3266 17.838
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] 0.008 0.008 -0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.79 r_lrange_it 13.605 r_lrange_other 13.594 r_dihedral_angle_3_deg 11.525 r_dihedral_angle_2_deg 8.827 r_dihedral_angle_1_deg 6.818 r_scangle_it 3.991 r_scangle_other 3.988 r_scbond_it 2.565 r_scbond_other 2.563
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.79 r_lrange_it 13.605 r_lrange_other 13.594 r_dihedral_angle_3_deg 11.525 r_dihedral_angle_2_deg 8.827 r_dihedral_angle_1_deg 6.818 r_scangle_it 3.991 r_scangle_other 3.988 r_scbond_it 2.565 r_scbond_other 2.563 r_mcangle_other 2.377 r_mcangle_it 2.37 r_angle_refined_deg 1.702 r_mcbond_it 1.575 r_mcbond_other 1.569 r_angle_other_deg 0.634 r_symmetry_nbd_refined 0.421 r_xyhbond_nbd_refined 0.418 r_nbd_refined 0.377 r_symmetry_xyhbond_nbd_refined 0.356 r_symmetry_nbd_other 0.309 r_nbd_other 0.283 r_nbtor_refined 0.182 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.061 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement