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1.95 Angstrom Resolution Crystal Structure of Fragment (35-274) of Membrane-bound Lytic Murein Transglycosylase F from Yersinia pestis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OWD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 Protein: 17.3 mg/ml, 0.01M Tris HCl (pH 8.3);
Screen: JCSG+ (H8), 0.2M Sodium chloride, 0.1 Bis-Tris (pH 5.5), 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.88 34.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.086 α = 90 b = 66.507 β = 90 c = 96.427 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 CCD MARMOSAIC 225 mm CCD C(111) 2016-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.95 30 100 0.11 0.11 0.045 29.5 7.2 30781 -3 27.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.98 100 0.7 0.7 0.277 0.895 3.2 7.3
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 4OWD 1.95 29.52 29200 1513 99.9 0.216 0.21327 0.26735 0.2688 RANDOM 35.574
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] 1.78 -2.23 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 12.493 r_dihedral_angle_3_deg 11.58 r_long_range_B_refined 6.952 r_long_range_B_other 6.894 r_scangle_other 5.114 r_mcangle_other 3.529 r_mcangle_it 3.528 r_dihedral_angle_1_deg 3.446 r_scbond_it 3.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.49 r_dihedral_angle_4_deg 12.493 r_dihedral_angle_3_deg 11.58 r_long_range_B_refined 6.952 r_long_range_B_other 6.894 r_scangle_other 5.114 r_mcangle_other 3.529 r_mcangle_it 3.528 r_dihedral_angle_1_deg 3.446 r_scbond_it 3.391 r_scbond_other 3.39 r_mcbond_it 2.449 r_mcbond_other 2.443 r_angle_refined_deg 1.504 r_angle_other_deg 0.87 r_chiral_restr 0.095 r_gen_planes_refined 0.023 r_gen_planes_other 0.02 r_bond_refined_d 0.012 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 3658 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing