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env2 cobalamin riboswitch aptamer domain in complex with ethynyl-4-(4-phenyl-2,3,4-triazole)-propanamine-cobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FRG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 303.15 10% (v/v) (+/-)-2-Methyl-2,4-pentanediol, 40 mM Sodium cacodylate trihydrate (pH 7.0), 12 mM Spermine tetrahydrochloride, 80 mM Potassium chloride, 20 mM Magnesium chloride hexahydrate. Hanging drop. 303.15 K.
Crystal Properties Matthews coefficient Solvent content 2.49 50.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.308 α = 90 b = 77.881 β = 90.94 c = 74.728 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 PILATUS 200K 2024-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE RIGAKU MICROMAX-003 1.54178
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 2.5 99 95.9 0.085 0.12 0.085 0.993 10.4 1.8 16193
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 2.5 2.54 43.6 0.231 0.327 0.231 0.883 1.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.55 20.41 1.34 15709 1581 98.75 0.2301 0.2244 0.2232 0.2809 0.2784
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.116 f_angle_d 0.615 f_chiral_restr 0.03 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3280 Solvent Atoms 257 Heterogen Atoms 259
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing