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BC2 nanobody in complex with the BC2 peptide tag
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IVO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 MES/imidazole, 2-Methyl-2,4-pentanediol, PEG 1000, PEG 3350, DL-Glutamatic acid monohydrate, DL-Alanine, Glycine, DL-Lysine monohydrochloride, DL-Serine
Crystal Properties Matthews coefficient Solvent content 1.76 30.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.01 α = 90 b = 31.53 β = 107.54 c = 35.88 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS3 6M 2014-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918409 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1 50.55 99.6 1 18.42 9.5 61121
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 1.03
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 5IVO 1 50.55 58063 3058 99.69 0.12908 0.128 0.1357 0.14961 0.1556 RANDOM 11.701
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] 0.46 -0.48 0.17 -0.27
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 68.402 r_dihedral_angle_2_deg 31.053 r_dihedral_angle_4_deg 20.613 r_sphericity_bonded 15.871 r_dihedral_angle_3_deg 13.094 r_long_range_B_refined 7.266 r_rigid_bond_restr 7.261 r_dihedral_angle_1_deg 7.182 r_long_range_B_other 7.086 r_mcangle_it 6.645
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 68.402 r_dihedral_angle_2_deg 31.053 r_dihedral_angle_4_deg 20.613 r_sphericity_bonded 15.871 r_dihedral_angle_3_deg 13.094 r_long_range_B_refined 7.266 r_rigid_bond_restr 7.261 r_dihedral_angle_1_deg 7.182 r_long_range_B_other 7.086 r_mcangle_it 6.645 r_mcangle_other 6.64 r_mcbond_other 5.343 r_mcbond_it 5.338 r_scangle_other 5.299 r_scbond_it 4.747 r_scbond_other 4.743 r_angle_refined_deg 1.549 r_angle_other_deg 1.095 r_chiral_restr 0.119 r_bond_refined_d 0.022 r_gen_planes_refined 0.013 r_gen_planes_other 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1042 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing