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Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 298 1.0M NA/K PHOSPHATE, pH 5.0, vapor diffusion, sitting drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.52 65.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.52 α = 90 b = 98.52 β = 90 c = 402.1 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 325 mm CCD 2007-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.4 50 91.7 0.086 86152 -3 57.73
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 2.8 2.9 91.7 0.767 2.2
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 2.8 47.67 55400 2813 97 0.194 0.192 0.1967 0.239 0.2402 RANDOM 50.77
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] -0.12 -0.06 -0.12 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.344 r_dihedral_angle_4_deg 16.752 r_dihedral_angle_3_deg 14.37 r_dihedral_angle_1_deg 5.581 r_scangle_it 1.189 r_angle_refined_deg 1.063 r_angle_other_deg 0.795 r_scbond_it 0.752 r_mcangle_it 0.479 r_mcbond_it 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.344 r_dihedral_angle_4_deg 16.752 r_dihedral_angle_3_deg 14.37 r_dihedral_angle_1_deg 5.581 r_scangle_it 1.189 r_angle_refined_deg 1.063 r_angle_other_deg 0.795 r_scbond_it 0.752 r_mcangle_it 0.479 r_mcbond_it 0.43 r_symmetry_hbond_refined 0.21 r_symmetry_vdw_refined 0.204 r_nbd_refined 0.203 r_symmetry_vdw_other 0.193 r_nbd_other 0.188 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.152 r_nbtor_other 0.081 r_chiral_restr 0.062 r_mcbond_other 0.053 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_xyhbond_nbd_other 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9740 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 44
Software Software Software Name Purpose XSCALE data scaling SHELX phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction SHELXD phasing