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Structure of Prolinyl-5'-O-adenosine phosphoramidate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFK 1AFK (using one molecule)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 PROTEIN WAS CRYSTALLIZED FROM 25%
PEG 3350, 20 MM SODIUM CITRATE, PH 5.5 Prolinyl-5'-O-adenosine phosphoramidate soaking was achieved as follows. 1 uL of a stock solution of 100 mM ligand was added to 2uL of reservoir solution, to achieve a concentration of ~33 mM in the soaking solution. A few RNase A crystals were soaked for 45 - 90 minutes in the soaking solution
Crystal Properties Matthews coefficient Solvent content 1.89 35.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.532 α = 90 b = 30.689 β = 90.56 c = 68.641 γ = 90
Symmetry Space Group C 1 2 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 CCD MARMOSAIC 300 mm CCD C(111) 2019-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.51 50 96.9 0.062 0.034 25.76 4.2 31473
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.56 83 0.588 0.372 1.38 3.1
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 1AFK (using one molecule) 1.51 49.31 29895 1576 96.47 0.1711 0.1687 0.1693 0.2171 0.216 RANDOM 26.492
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] -0.25 -0.11 1.9 -1.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.973 r_dihedral_angle_3_deg 15.548 r_dihedral_angle_1_deg 7.368 r_dihedral_angle_4_deg 7.243 r_angle_refined_deg 1.348 r_chiral_restr 0.107 r_gen_planes_refined 0.014 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing