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Spectroscopic and structural characterization of a genetically encoded direct sensor for protein-ligand interactions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 298 500 ul of 0.1 M Citric Acid, pH 3.5, 3M NaCl in reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop. Crystals were soaked to pH 5.5 overnight with 3 exchanges
Crystal Properties Matthews coefficient Solvent content 2.16 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.209 α = 90 b = 93.11 β = 90 c = 104.369 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 PILATUS3 6M Si(111) and Si(220) double crystal 2019-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.84 69.48 99.2 0.998 16.7 7.1 19561
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 1.84 9.03 0.951
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3RY2 1.84 69.48 18589 969 98.4 0.1759 0.1739 0.1833 0.2127 0.2198 RANDOM 20.68
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] 0.06 1.88 -1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.226 r_dihedral_angle_4_deg 20.062 r_dihedral_angle_3_deg 13.325 r_dihedral_angle_1_deg 7.905 r_angle_other_deg 4.015 r_mcangle_it 3.264 r_mcbond_it 2.223 r_mcbond_other 2.219 r_angle_refined_deg 2.051 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.226 r_dihedral_angle_4_deg 20.062 r_dihedral_angle_3_deg 13.325 r_dihedral_angle_1_deg 7.905 r_angle_other_deg 4.015 r_mcangle_it 3.264 r_mcbond_it 2.223 r_mcbond_other 2.219 r_angle_refined_deg 2.051 r_chiral_restr 0.12 r_bond_refined_d 0.02 r_gen_planes_other 0.018 r_gen_planes_refined 0.01 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1837 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction pointless data scaling PHASER phasing