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Molecular scaffolds expand the nanobody toolkit for cryo-EM applications: crystal structure of Mb-cHopQ-Nb207
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 293 0.2 M ammonium citrate, 17 % PEG3350, 10 % Glycerol
Crystal Properties Matthews coefficient Solvent content 2.58 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.17 α = 92.05 b = 92.92 β = 96.93 c = 244.22 γ = 112.15
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 2017-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976230 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.84 41.45 95.6 0.039 0.055 0.999 11.65 1.78 129248 97.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.84 2.9 94.5 0.469 0.663 0.854 1.45 1.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.84 41.45 129248 6538 95.5 0.206 0.204 0.2257 0.239 0.252 RANDOM 99.89
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] -4.4392 -1.3114 1.5186 1.9321 -0.4157 2.507
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.15 t_omega_torsion 2.69 t_angle_deg 1.26 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 23.15 t_omega_torsion 2.69 t_angle_deg 1.26 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33038 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 1
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing