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Convergent solutions to VHH domain stabilization from natural and in vitro evolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HCV PDB entry 1HCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 30% PEG 4K, 0.3M Ammonium Sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.211 α = 90 b = 120.711 β = 103.32 c = 52.246 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 193 CCD SBC-3 2003-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.0332 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 20 99.7 0.091 0.091 7.6 3.6 32402 32305 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 99.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 entry 1HCV 1.9 20 32305 30610 1635 99.62 0.18803 0.18546 0.2361 0.2339 RANDOM 17.292
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] 0.3 -0.49 -0.48 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.38 r_scangle_it 5.032 r_mcangle_it 4.465 r_scbond_it 3.621 r_mcbond_it 2.988 r_angle_refined_deg 1.238 r_angle_other_deg 0.905 r_symmetry_vdw_other 0.311 r_nbd_other 0.255 r_symmetry_hbond_refined 0.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.38 r_scangle_it 5.032 r_mcangle_it 4.465 r_scbond_it 3.621 r_mcbond_it 2.988 r_angle_refined_deg 1.238 r_angle_other_deg 0.905 r_symmetry_vdw_other 0.311 r_nbd_other 0.255 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.156 r_chiral_restr 0.113 r_nbtor_other 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3510 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing