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A2.3 Nanobody In Complex With Microcystin-LR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 25% w/v PEG MME 3350, 200 mM ammonium sulfate, 100 mM HEPES
Crystal Properties Matthews coefficient Solvent content 2.51 50.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.097 α = 90 b = 101.317 β = 90 c = 102.412 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2018-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979460 SSRL BL9-2
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 2.35 36.01 99.1 0.067 0.082 0.046 0.998 12.9 5.4 17031
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.43 0.997 0.68
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.35 35.685 16990 847 98.693 0.238 0.2357 0.242 0.2801 0.2822 0.05 60.214
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] 0.013 0.125 -0.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.555 r_lrange_it 17.119 r_lrange_other 17.115 r_dihedral_angle_6_deg 15.529 r_scangle_it 11.001 r_scangle_other 10.999 r_mcangle_it 9.66 r_mcangle_other 9.659 r_dihedral_angle_1_deg 9.415 r_dihedral_angle_2_deg 9.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.555 r_lrange_it 17.119 r_lrange_other 17.115 r_dihedral_angle_6_deg 15.529 r_scangle_it 11.001 r_scangle_other 10.999 r_mcangle_it 9.66 r_mcangle_other 9.659 r_dihedral_angle_1_deg 9.415 r_dihedral_angle_2_deg 9.127 r_scbond_it 7.561 r_scbond_other 7.559 r_mcbond_it 7.2 r_mcbond_other 7.198 r_angle_refined_deg 1.92 r_angle_other_deg 0.657 r_nbd_refined 0.278 r_xyhbond_nbd_refined 0.275 r_symmetry_nbd_other 0.242 r_symmetry_xyhbond_nbd_refined 0.22 r_nbd_other 0.2 r_nbtor_refined 0.195 r_symmetry_xyhbond_nbd_other 0.188 r_symmetry_nbd_refined 0.147 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.078 r_xyhbond_nbd_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2768 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing