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Structure of Lytic Transglycosylase MltE mutant S73A from E.coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y8P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 20% Ethanol and 0.1 M TRIS HCl (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.14 42.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.621 α = 90 b = 56.621 β = 90 c = 111.347 γ = 90
Symmetry Space Group P 41 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 DECTRIS PILATUS 6M 2016-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979210 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.38 48.15 99.6 0.018 19.92 8.8 38055
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 1.38 1.43
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 2Y8P 1.38 40.07 36042 1873 99.6 0.18816 0.18675 0.1872 0.2142 0.2134 RANDOM 18.942
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] 0.25 0.25 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.485 r_dihedral_angle_4_deg 20.161 r_dihedral_angle_3_deg 14.276 r_long_range_B_refined 7.178 r_long_range_B_other 6.304 r_dihedral_angle_1_deg 6.016 r_scangle_other 4.068 r_scbond_it 2.857 r_scbond_other 2.857 r_mcangle_other 2.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.485 r_dihedral_angle_4_deg 20.161 r_dihedral_angle_3_deg 14.276 r_long_range_B_refined 7.178 r_long_range_B_other 6.304 r_dihedral_angle_1_deg 6.016 r_scangle_other 4.068 r_scbond_it 2.857 r_scbond_other 2.857 r_mcangle_other 2.495 r_mcangle_it 2.484 r_angle_refined_deg 1.883 r_mcbond_it 1.73 r_mcbond_other 1.648 r_angle_other_deg 1.131 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 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 1466 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing