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Structural evidence of thioacetate reduction by fluorescent protein mRuby-( mRuby-thioacetate structure2 )
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9V58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 ~2 M Sodium formate, ~12% % w/v PEG3350, ~0.2M thioacetate.
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.42 α = 90 b = 66.937 β = 90 c = 95.454 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 PILATUS3 6M 2025-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL18U 0.978530 NFPSS BL18U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 50 100 0.0943 0.0286 0.9995 28 11.5 33138
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 100 0.6323 6.97
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 1.5 47.77 32776 295 99.9 0.20992 0.2096 0.2174 0.24452 0.2517 RANDOM 19.568
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] 0.75 -0.45 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.313 r_dihedral_angle_1_deg 8.107 r_dihedral_angle_2_deg 6.374 r_long_range_B_refined 4.391 r_long_range_B_other 4.39 r_scangle_other 2.962 r_mcangle_it 1.784 r_mcangle_other 1.783 r_scbond_it 1.768 r_scbond_other 1.756
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.313 r_dihedral_angle_1_deg 8.107 r_dihedral_angle_2_deg 6.374 r_long_range_B_refined 4.391 r_long_range_B_other 4.39 r_scangle_other 2.962 r_mcangle_it 1.784 r_mcangle_other 1.783 r_scbond_it 1.768 r_scbond_other 1.756 r_angle_refined_deg 1.285 r_mcbond_it 1.07 r_mcbond_other 1.069 r_angle_other_deg 0.498 r_chiral_restr 0.078 r_gen_planes_refined 0.005 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1719 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement Aimless data scaling autoPX data reduction MOLREP phasing PDB_EXTRACT data extraction