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2.6 Angstrom Resolution Crystal Structure of Stage II Sporulation Protein D (SpoIID) from Clostridium difficile in Complex with Triacetylchitotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RWR PDB-4RWR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 291 Protein: 7.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 7.2), 2mM NAG3, 1/100 Elostase; Screen: JCSG+ (B11), 1.6M tri-Sodium citrate pH 6.6
Crystal Properties Matthews coefficient Solvent content 4.05 69.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.082 α = 90 b = 98.082 β = 90 c = 108.327 γ = 120
Symmetry Space Group P 31 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) 2014-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 2.6 30 99.9 0.067 0.067 0.903 30.8 8.8 18969 -3 69.1
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 2.6 2.64 100 0.608 4.1 9.3
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 PDB-4RWR 2.6 29.08 17967 976 99.81 0.15671 0.15461 0.19629 0.2012 RANDOM 69.176
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] -0.92 -0.46 -0.92 2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.644 r_dihedral_angle_4_deg 11.809 r_dihedral_angle_3_deg 10.446 r_long_range_B_refined 8.781 r_long_range_B_other 8.729 r_scangle_other 6.701 r_scbond_it 4.271 r_scbond_other 4.224 r_mcangle_it 3.61 r_mcangle_other 3.608
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.644 r_dihedral_angle_4_deg 11.809 r_dihedral_angle_3_deg 10.446 r_long_range_B_refined 8.781 r_long_range_B_other 8.729 r_scangle_other 6.701 r_scbond_it 4.271 r_scbond_other 4.224 r_mcangle_it 3.61 r_mcangle_other 3.608 r_dihedral_angle_1_deg 2.939 r_mcbond_it 2.416 r_mcbond_other 2.416 r_angle_refined_deg 1.477 r_angle_other_deg 0.853 r_chiral_restr 0.088 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.011 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 2280 Nucleic Acid Atoms Solvent Atoms 147 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing