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Structure of Glutamyl-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 PROTEIN WAS CRYSTALLIZED FROM 25 percent PEG 3350, 20 MM SODIUM CITRATE, PH 5.5. Glutaminyl-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 ~35 mM in the soaking solution. A few RNase A crystals were soaked for 110 - 130 minutes in the soaking solution.
Crystal Properties Matthews coefficient Solvent content 2.25 45.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.255 α = 90 b = 32.957 β = 90.43 c = 73.987 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 2023-01-17 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 1.76 19.93 98.9 0.0949 22.18 20 24382
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 1.76 1.86 93.9 0.701 2.59 7.08
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 1.76 19.93 22845 1168 97.39 0.21066 0.20874 0.2181 0.24935 0.2546 RANDOM 31.693
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] -0.7 -0.36 -0.32 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.027 r_long_range_B_refined 8.806 r_long_range_B_other 8.803 r_dihedral_angle_2_deg 8.318 r_dihedral_angle_1_deg 7.711 r_scangle_other 7.367 r_mcangle_it 5.512 r_mcangle_other 5.492 r_scbond_it 4.912 r_scbond_other 4.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.027 r_long_range_B_refined 8.806 r_long_range_B_other 8.803 r_dihedral_angle_2_deg 8.318 r_dihedral_angle_1_deg 7.711 r_scangle_other 7.367 r_mcangle_it 5.512 r_mcangle_other 5.492 r_scbond_it 4.912 r_scbond_other 4.91 r_mcbond_it 3.961 r_mcbond_other 3.961 r_angle_refined_deg 1.193 r_angle_other_deg 0.449 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_dihedral_angle_4_deg r_gen_planes_other 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 1893 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing