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Real-space refinement for the hen egg-white lysozyme structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 277.15 NaCl, Acetic-sodium acetate buffer
Crystal Properties Matthews coefficient Solvent content 1.96 37.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.137 α = 90 b = 78.137 β = 90 c = 36.864 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 RIGAKU HyPix-6000HE 2024-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 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 1.3 21.28 100 1 22.3 9.7 28690
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 0.513
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1.3 21.28 27195 1448 99.94 0.18702 0.18586 0.1945 0.20878 0.2191 RANDOM 13.056
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.344 r_dihedral_angle_2_deg 7.33 r_dihedral_angle_1_deg 6.413 r_long_range_B_refined 5.604 r_long_range_B_other 5.022 r_scangle_other 3.387 r_scbond_it 2.175 r_scbond_other 2.174 r_angle_refined_deg 1.937 r_mcangle_it 1.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.344 r_dihedral_angle_2_deg 7.33 r_dihedral_angle_1_deg 6.413 r_long_range_B_refined 5.604 r_long_range_B_other 5.022 r_scangle_other 3.387 r_scbond_it 2.175 r_scbond_other 2.174 r_angle_refined_deg 1.937 r_mcangle_it 1.706 r_mcangle_other 1.705 r_mcbond_it 1.191 r_mcbond_other 1.169 r_angle_other_deg 0.649 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling REFMAC phasing