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Crystal structure of hen egg white lysozyme at 100 Kelvin with Apiezon T
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 sodium chloride, 100 mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.96 37.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.823 α = 90 b = 77.823 β = 90 c = 37.031 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 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 1.497 25.361 99 0.99 17 1 18791
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 10 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 1.497 25.361 18791 979 99.539 0.222 0.2205 0.228 0.2497 0.2598 14.245
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] 0.013 0.013 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.095 r_dihedral_angle_3_deg 12.014 r_dihedral_angle_1_deg 6.941 r_dihedral_angle_2_deg 6.928 r_lrange_it 4.48 r_lrange_other 4.465 r_scangle_it 3.441 r_scangle_other 3.439 r_scbond_it 2.241 r_scbond_other 2.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.095 r_dihedral_angle_3_deg 12.014 r_dihedral_angle_1_deg 6.941 r_dihedral_angle_2_deg 6.928 r_lrange_it 4.48 r_lrange_other 4.465 r_scangle_it 3.441 r_scangle_other 3.439 r_scbond_it 2.241 r_scbond_other 2.239 r_mcangle_it 1.883 r_mcangle_other 1.883 r_angle_refined_deg 1.832 r_mcbond_it 1.306 r_mcbond_other 1.301 r_angle_other_deg 0.65 r_xyhbond_nbd_refined 0.38 r_symmetry_xyhbond_nbd_refined 0.269 r_nbd_refined 0.258 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.153 r_nbd_other 0.151 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.027 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 87 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement