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Structure of Lytic Transglycosylase MltC from Escherichia coli in complex with tetrasaccharide at 2.9 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C5F PDB ENTRY 4C5F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 18% PEG 3350, 0.2M TRI-AMMONIUM CITRATE PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.206 α = 90 b = 112.814 β = 93.52 c = 61.571 γ = 90
Symmetry Space Group P 1 21 1
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 2013-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 45.03 99.8 0.14 3.6 4.2 18455 2
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 2.7 2.83 99.6 0.47 1.8 3.9
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 PDB ENTRY 4C5F 2.9 14.93 14033 741 98.94 0.19643 0.19242 0.1987 0.26949 0.2767 RANDOM 36.26
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] 2.24 -3.53 -1.06 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.993 r_dihedral_angle_3_deg 20.032 r_dihedral_angle_4_deg 19.756 r_dihedral_angle_1_deg 7.182 r_mcangle_it 2.097 r_angle_refined_deg 1.509 r_mcbond_it 1.173 r_mcbond_other 1.172 r_scbond_it 1.039 r_angle_other_deg 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.993 r_dihedral_angle_3_deg 20.032 r_dihedral_angle_4_deg 19.756 r_dihedral_angle_1_deg 7.182 r_mcangle_it 2.097 r_angle_refined_deg 1.509 r_mcbond_it 1.173 r_mcbond_other 1.172 r_scbond_it 1.039 r_angle_other_deg 0.81 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 5154 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC model building SCALA data scaling iMOSFLM phasing SCALA phasing MOLREP phasing REFMAC phasing REFMAC refinement