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Structure of the GFP:GFP-nanobody complex from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 7D30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M Na2SO4, 0.1M Bis-Tris propane pH6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.98 37.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.544 α = 90 b = 88.363 β = 90 c = 122.842 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS EIGER X 9M 2023-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.953729 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 44.221 100 0.166 11.5 13.4 25324
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 1.083
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.1 44.221 25322 1267 99.964 0.165 0.1623 0.1732 0.2092 0.2223 35.475
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] 2.096 1.094 -3.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.995 r_dihedral_angle_3_deg 12.519 r_lrange_other 8.54 r_lrange_it 8.524 r_dihedral_angle_1_deg 7.499 r_dihedral_angle_2_deg 7.09 r_scangle_it 6.254 r_scangle_other 6.252 r_mcangle_it 4.794 r_mcangle_other 4.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.995 r_dihedral_angle_3_deg 12.519 r_lrange_other 8.54 r_lrange_it 8.524 r_dihedral_angle_1_deg 7.499 r_dihedral_angle_2_deg 7.09 r_scangle_it 6.254 r_scangle_other 6.252 r_mcangle_it 4.794 r_mcangle_other 4.793 r_scbond_it 4.016 r_scbond_other 4.015 r_mcbond_it 3.105 r_mcbond_other 3.103 r_angle_refined_deg 1.454 r_angle_other_deg 0.491 r_symmetry_nbd_refined 0.223 r_symmetry_nbd_other 0.198 r_nbd_refined 0.193 r_nbd_other 0.185 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.104 r_symmetry_nbtor_other 0.091 r_chiral_restr 0.065 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2630 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing