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Crystal structure of NB7, a nanobody targeting prostate specific membrane antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M7Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.7M (NH4)2SO4,
6.57% 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.99 58.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.563 α = 90 b = 171.716 β = 91.81 c = 83.479 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 100 PIXEL DECTRIS PILATUS3 S 6M 2017-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.65 47.2 98.92 0.067 0.993 8.49 4.5 45149
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.77 0.485
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 5M7Q 2.65 47.2 1.34 43210 2120 98.93 0.1844 0.182 0.1878 0.2309 0.2312
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 12.525 f_angle_d 1.645 f_chiral_restr 0.072 f_bond_d 0.012 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7615 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing