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Lytic transglycosylase in action
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YIM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 277.15 100 mM CHES pH 9.5, 100 mM tri sodium citrate, 30% PEG 3000
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.714 α = 90 b = 72.681 β = 90 c = 124.924 γ = 90
Symmetry Space Group P 21 21 21
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 PSI PILATUS 6M 2016-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.1 SOLEIL PROXIMA 1
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 1.43 49.15 97.6 0.185 9.3 110458
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4YIM 1.43 49.15 108023 2002 97.38 0.19199 0.19138 0.1903 0.22578 0.2254 RANDOM 24.892
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 14.141 r_long_range_B_refined 6.207 r_dihedral_angle_1_deg 5.018 r_scbond_it 3.649 r_mcangle_it 2.703 r_mcbond_it 2.079 r_angle_refined_deg 1.591 r_chiral_restr 0.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_4_deg 18.333 r_dihedral_angle_3_deg 14.141 r_long_range_B_refined 6.207 r_dihedral_angle_1_deg 5.018 r_scbond_it 3.649 r_mcangle_it 2.703 r_mcbond_it 2.079 r_angle_refined_deg 1.591 r_chiral_restr 0.199 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4479 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction