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Structure of Histidine-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, pH 5.5,
Histidyl-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 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.829 α = 90 b = 32.807 β = 90.18 c = 74.156 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 2023-01-19 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 2 19.85 99 0.1384 10.69 9.91 16652
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 2 2.1 98.6 0.609 2.63 7.6
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 2 19.85 15581 903 98.04 0.24519 0.24203 0.2495 0.3009 0.3117 RANDOM 35.57
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] -0.65 -0.52 -0.38 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.424 r_dihedral_angle_2_deg 11.379 r_long_range_B_other 9.659 r_long_range_B_refined 9.651 r_dihedral_angle_1_deg 7.908 r_scangle_other 6.296 r_mcangle_it 5.845 r_mcangle_other 5.834 r_scbond_it 4.01 r_scbond_other 4.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.424 r_dihedral_angle_2_deg 11.379 r_long_range_B_other 9.659 r_long_range_B_refined 9.651 r_dihedral_angle_1_deg 7.908 r_scangle_other 6.296 r_mcangle_it 5.845 r_mcangle_other 5.834 r_scbond_it 4.01 r_scbond_other 4.008 r_mcbond_it 3.744 r_mcbond_other 3.743 r_angle_refined_deg 0.979 r_angle_other_deg 0.356 r_chiral_restr 0.047 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 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 1902 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling MOLREP phasing