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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 6.5 298 500 ul of 0.1 M Bis-Tris, pH 6.5, 25% w/v polyethylene glycol 3350 in the reservoir with 2 ul of reservoir buffer mixed with 2 ul of 10 mg/ml of protein in the drop
Crystal Properties Matthews coefficient Solvent content 1.97 37.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.458 α = 90 b = 85.555 β = 99 c = 58.098 γ = 90
Symmetry Space Group P 1 21 1
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 2018-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.000 ALS 5.0.2
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 1.55 42.78 99.6 0.923 10.9 1 64849
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 1.55 1.58 0.938 1.3
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 1.55 42.78 62823 2000 99.55 0.167 0.1659 0.1673 0.2014 0.203 RANDOM 28.433
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] 0.12 -0.31 1.85 -1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.473 r_dihedral_angle_4_deg 19.673 r_dihedral_angle_3_deg 13.686 r_dihedral_angle_1_deg 7.28 r_angle_refined_deg 2.147 r_chiral_restr 0.172 r_bond_refined_d 0.022 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3590 Nucleic Acid Atoms Solvent Atoms 451 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling PHASER phasing