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Structure of Lytic Transglycosylase MltE mutant S75A 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 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.636 α = 90 b = 56.636 β = 90 c = 110.434 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 2016-10-19 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 1.35 40.05 100 0.018 18.2 13.3 40280
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 1.35 1.4
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 1.35 40.05 38260 2020 100 0.18583 0.18425 0.1855 0.21554 0.2152 RANDOM 19.69
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] 0.39 0.39 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.832 r_dihedral_angle_4_deg 21.296 r_dihedral_angle_3_deg 15.517 r_long_range_B_refined 7.136 r_long_range_B_other 6.78 r_dihedral_angle_1_deg 6.284 r_scangle_other 4.681 r_scbond_it 3.198 r_scbond_other 3.197 r_mcangle_other 2.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.832 r_dihedral_angle_4_deg 21.296 r_dihedral_angle_3_deg 15.517 r_long_range_B_refined 7.136 r_long_range_B_other 6.78 r_dihedral_angle_1_deg 6.284 r_scangle_other 4.681 r_scbond_it 3.198 r_scbond_other 3.197 r_mcangle_other 2.598 r_mcangle_it 2.595 r_mcbond_it 1.83 r_mcbond_other 1.756 r_angle_refined_deg 1.711 r_angle_other_deg 1.086 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.006 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 1461 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing