☰ Navigation Tabs
2.05 Angstrom Resolution Crystal Structure of Peptidoglycan-Binding Protein from Clostridioides difficile in Complex with Glutamine Hydroxamate.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Protein: 7.8 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3),
Screen: JCSG+ (B3), 0.1M Bicine (pH 8.5), 20% (w/v) PEG 6000.
Crystal Properties Matthews coefficient Solvent content 2.41 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.949 α = 90 b = 35.008 β = 126.25 c = 101.533 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 300 mm CCD C(111) 2014-06-04 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) 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 2.05 29.08 100 0.093 0.093 28.1 5 24487 -3 32.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 99.9 0.769 0.769 2.06 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.05 29.08 23265 1199 99.76 0.17346 0.17155 0.1763 0.2103 0.2139 RANDOM 48.198
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] 3.25 1.15 -2.9 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.864 r_dihedral_angle_3_deg 8.916 r_dihedral_angle_4_deg 8.577 r_long_range_B_refined 6.114 r_long_range_B_other 5.992 r_scangle_other 2.715 r_dihedral_angle_1_deg 2.636 r_mcangle_it 2.425 r_mcangle_other 2.425 r_scbond_it 1.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.864 r_dihedral_angle_3_deg 8.916 r_dihedral_angle_4_deg 8.577 r_long_range_B_refined 6.114 r_long_range_B_other 5.992 r_scangle_other 2.715 r_dihedral_angle_1_deg 2.636 r_mcangle_it 2.425 r_mcangle_other 2.425 r_scbond_it 1.642 r_scbond_other 1.637 r_mcbond_it 1.444 r_mcbond_other 1.441 r_angle_refined_deg 1.313 r_angle_other_deg 0.817 r_chiral_restr 0.079 r_gen_planes_refined 0.022 r_gen_planes_other 0.018 r_bond_refined_d 0.008 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 2460 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing