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Crystal structure of lysozyme from Equus asinus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EL1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-tris
Crystal Properties Matthews coefficient Solvent content 2.42 49.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.543 α = 90 b = 57.543 β = 90 c = 73.359 γ = 120
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 DECTRIS PILATUS 6M 2017-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17B1 0.97775 SSRF BL17B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.76 50 99.9 19.562 5 26974
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.79
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1EL1 1.76 49.83 25433 1348 99.39 0.19407 0.19268 0.22083 0.2099 RANDOM 22.182
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] 0.04 0.02 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 15.731 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 5.321 r_long_range_B_other 5.277 r_mcangle_it 2.635 r_mcangle_other 2.635 r_scangle_other 2.497 r_scbond_it 1.479
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.69 r_dihedral_angle_4_deg 15.731 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_1_deg 6.385 r_long_range_B_refined 5.321 r_long_range_B_other 5.277 r_mcangle_it 2.635 r_mcangle_other 2.635 r_scangle_other 2.497 r_scbond_it 1.479 r_scbond_other 1.478 r_mcbond_it 1.458 r_mcbond_other 1.457 r_angle_refined_deg 1.303 r_angle_other_deg 0.98 r_chiral_restr 0.093 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2026 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing