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Structure of Butyl-5'-O-adenosine phosphoramidate/RNase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 25% PEG 3350, 20 MM SODIUM CITRATE
PROTEIN WAS CRYSTALLIZED FROM 25%
PEG 3350, 20 MM SODIUM CITRATE, PH 5.5
Butyl-5'-O-adenosine phosphoramidate was soaked into the crystals using a stock solution of 100 mM, to achieve ~35 mM in the soaking solution.
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.027 α = 90 b = 32.123 β = 90.71 c = 72.425 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 PIXEL Bruker PHOTON II 2023-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.53 19.57 99.5 0.089 11.74 8.2 35060
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.63 99.4 0.601 1.1 3.88
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 1.53 19.57 31580 1595 94.17 0.24773 0.2453 0.2539 0.29675 0.3034 RANDOM 23.26
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] -0.76 -0.27 0.61 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.705 r_dihedral_angle_1_deg 7.038 r_long_range_B_refined 6.004 r_long_range_B_other 5.985 r_dihedral_angle_2_deg 5.742 r_scangle_other 4.035 r_mcangle_it 3.205 r_mcangle_other 3.204 r_scbond_it 2.547 r_scbond_other 2.546
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.705 r_dihedral_angle_1_deg 7.038 r_long_range_B_refined 6.004 r_long_range_B_other 5.985 r_dihedral_angle_2_deg 5.742 r_scangle_other 4.035 r_mcangle_it 3.205 r_mcangle_other 3.204 r_scbond_it 2.547 r_scbond_other 2.546 r_mcbond_it 2.062 r_mcbond_other 2.036 r_angle_refined_deg 1.489 r_angle_other_deg 0.49 r_chiral_restr 0.066 r_gen_planes_refined 0.008 r_bond_refined_d 0.006 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 1876 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing