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Crystal structure of the biphotochromic fluorescent protein SAASoti (C21N/V127T variant) in its green on-state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6NQP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.1 M Tris pH 8.0; 30% w/v Polyethylene glycol monomethyl ether 2,000
Crystal Properties Matthews coefficient Solvent content 2.27 45.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.583 α = 90 b = 104.583 β = 90 c = 151.187 γ = 120
Symmetry Space Group P 61 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 RIGAKU HyPix-6000HE 2023-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
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 3 24.28 98 0.705 0.719 0.135 0.985 7.1 26.9 10148
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 3 3.18 92.6 4.746 4.83 0.884 0.601 28.8
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 MOLECULAR REPLACEMENT THROUGHOUT 3 23.85 9579 517 97.73 0.29356 0.29114 0.2916 0.34012 0.3387 RANDOM 65.87
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] 0.71 0.35 0.71 -2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.562 r_dihedral_angle_2_deg 17.441 r_dihedral_angle_1_deg 8.568 r_long_range_B_refined 4.184 r_long_range_B_other 4.184 r_angle_refined_deg 2.054 r_scangle_other 1.992 r_mcangle_it 1.901 r_mcangle_other 1.9 r_scbond_it 1.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.562 r_dihedral_angle_2_deg 17.441 r_dihedral_angle_1_deg 8.568 r_long_range_B_refined 4.184 r_long_range_B_other 4.184 r_angle_refined_deg 2.054 r_scangle_other 1.992 r_mcangle_it 1.901 r_mcangle_other 1.9 r_scbond_it 1.147 r_scbond_other 1.147 r_mcbond_it 1.095 r_mcbond_other 1.095 r_angle_other_deg 0.816 r_chiral_restr 0.112 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_bond_other_d 0.004 r_gen_planes_other 0.003 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3463 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing