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The apo form of the triclocarban-binding single domain camelid nanobody VHH T9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other T9 holo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 protein concentration 40 mg/ml
well 25% w/v PEG MME 3350, 200 mM ammonium sulfate, 100 mM Hepes
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.814 α = 90 b = 48.814 β = 90 c = 119.28 γ = 90
Symmetry Space Group P 43 2 2
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 DECTRIS PILATUS3 S 6M 2017-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
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 1.35 48.81 100 0.031 24.5 6.8 32653
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 1.35 1.39 99.9 0.624 2.4
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 T9 holo 1.35 48.81 30970 1622 99.9 0.16314 0.16177 0.1619 0.18887 0.1895 RANDOM 25.44
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] 0.35 0.35 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.833 r_sphericity_free 23.137 r_dihedral_angle_4_deg 21.082 r_sphericity_bonded 12.68 r_dihedral_angle_3_deg 9.679 r_dihedral_angle_1_deg 5.583 r_scangle_other 5.095 r_scbond_other 4.474 r_scbond_it 4.47 r_long_range_B_refined 4.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.833 r_sphericity_free 23.137 r_dihedral_angle_4_deg 21.082 r_sphericity_bonded 12.68 r_dihedral_angle_3_deg 9.679 r_dihedral_angle_1_deg 5.583 r_scangle_other 5.095 r_scbond_other 4.474 r_scbond_it 4.47 r_long_range_B_refined 4.35 r_long_range_B_other 4.331 r_mcangle_other 2.706 r_mcangle_it 2.705 r_rigid_bond_restr 2.616 r_mcbond_it 2.104 r_mcbond_other 2.046 r_angle_refined_deg 1.395 r_angle_other_deg 0.745 r_chiral_restr 0.088 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 933 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing