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The hapten triclocarban bound to the single domain camelid nanobody VHH T10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VM0 apo T9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 protein was 21 mg/ml
well contained 1.3 M ammonium sulfate, 100 mM citric acid
Crystal Properties Matthews coefficient Solvent content 1.84 33.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.769 α = 90 b = 36.387 β = 111.18 c = 44.598 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2016-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97947 SSRL BL7-1
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 1.5 41.9 98.2 0.071 10.4 2.6 17461
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 1.5 1.53 95 0.4 2.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT apo T9 1.5 41.59 16901 551 98.06 0.17233 0.17166 0.1714 0.1931 0.1922 RANDOM 9.333
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] -0.42 0.17 -0.61 0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.983 r_dihedral_angle_4_deg 19.934 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 6.221 r_long_range_B_refined 3.494 r_long_range_B_other 3.323 r_scangle_other 2.049 r_angle_refined_deg 1.593 r_scbond_it 1.374 r_scbond_other 1.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.983 r_dihedral_angle_4_deg 19.934 r_dihedral_angle_3_deg 11.899 r_dihedral_angle_1_deg 6.221 r_long_range_B_refined 3.494 r_long_range_B_other 3.323 r_scangle_other 2.049 r_angle_refined_deg 1.593 r_scbond_it 1.374 r_scbond_other 1.331 r_mcangle_other 1.172 r_mcangle_it 1.171 r_angle_other_deg 0.755 r_mcbond_it 0.714 r_mcbond_other 0.684 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 989 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing