☰ Navigation Tabs
env2 cobalamin riboswitch aptamer domain in complex with ethynyl-4-(4-phenyl-2,3,4-triazole)-guanidinium-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 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.206 α = 90 b = 78.205 β = 90.44 c = 77.101 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 2024-09-12 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) 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 2.19 20 98.7 0.078 0.043 0.99 15.5 3.1 25509
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 2.2 2.28 91.1 0.191 0.237 0.138 0.944 2.7
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 2.19 19.73 1.34 25227 1991 97.16 0.229 0.2247 0.2252 0.2787 0.2788
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 15.459 f_angle_d 0.552 f_chiral_restr 0.026 f_plane_restr 0.003 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 3280 Solvent Atoms 340 Heterogen Atoms 269
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing