☰ Navigation Tabs
High resolution structure of the functional region of Cwp19 from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 90% (10 mM monobasic potassium phosphate, 18% PEG 8,000)
10% (20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine
Crystal Properties Matthews coefficient Solvent content 2.37 48.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.016 α = 90 b = 65.639 β = 90 c = 104.01 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 PIXEL DECTRIS PILATUS 6M-F 2016-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 65.64 99.5 0.118 0.123 0.033 0.999 15.4 25.5 93318
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 100 0.674 0.704 0.2 0.982 3.7 23.7
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 5OQ2 1.35 55.51 91316 1916 99.44 0.14958 0.14906 0.17415 0.1874 RANDOM 15.682
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] -1.11 3.26 -2.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.815 r_sphericity_free 24.764 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_4_deg 11.421 r_sphericity_bonded 9.681 r_dihedral_angle_1_deg 6.07 r_long_range_B_refined 3.187 r_long_range_B_other 2.962 r_scangle_other 2.392 r_mcangle_other 2.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.815 r_sphericity_free 24.764 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_4_deg 11.421 r_sphericity_bonded 9.681 r_dihedral_angle_1_deg 6.07 r_long_range_B_refined 3.187 r_long_range_B_other 2.962 r_scangle_other 2.392 r_mcangle_other 2.253 r_mcangle_it 2.243 r_scbond_it 2.107 r_scbond_other 2.091 r_rigid_bond_restr 1.881 r_mcbond_it 1.793 r_mcbond_other 1.766 r_angle_refined_deg 1.534 r_angle_other_deg 0.974 r_chiral_restr 0.106 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2883 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing