☰ Navigation Tabs
Structure of VHH R419 isolated from a pre-immune phage display library
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6DBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.2 M ammonium sulfate
0.1 M MES
30% PEG MME
Crystal Properties Matthews coefficient Solvent content 2.81 56.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.281 α = 90 b = 58.281 β = 90 c = 155.358 γ = 120
Symmetry Space Group P 65 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 RAYONIX MX-300 2013-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 36.145 99.2 0.207 0.218 0.067 10.7 10.1 25716 19.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 91.5 0.335 0.335 0.359 0.126 2 7.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6DBA 1.5 36.145 1.39 25678 1310 99.04 0.1767 0.176 0.1775 0.1903 0.1913
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.719 f_angle_d 0.875 f_chiral_restr 0.053 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 853 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement SCALA data scaling PDB_EXTRACT data extraction xia2 data reduction PHASER phasing