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Crystal Structure of Nanobody VHH222 Specific for PA14 Cif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZJ 3EZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292.8 100 mM succinic acid/sodium phosphate monobasic/glycine 2:7:7 (SPG) pH 6.0, 25% (w/v) PEG1500
Crystal Properties Matthews coefficient Solvent content 2.73 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.006 α = 90 b = 58.006 β = 90 c = 75.935 γ = 120
Symmetry Space Group P 31 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 EIGER X 16M 2020-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.978636 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.9 41.9 99.48 0.07468 0.07902 0.02545 0.999 16.76 9.5 12038 35.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.968 97.35 1.286 1.379 0.4838 0.838 1.58 7.6
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 FREE R-VALUE 3EZJ 1.9 41.9 1.37 12013 598 99.49 0.2126 0.212 0.212 0.2242 0.2242 42.92
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 13.9787 f_angle_d 0.8185 f_chiral_restr 0.0626 f_bond_d 0.0098 f_plane_restr 0.0031
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 881 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing PHENIX refinement Coot model building