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Structure of Adenosine monophosphate/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.
5'-O-adenosine monophoshate 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 160 - 180 minutes in the soaking solution
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.054 α = 90 b = 32.514 β = 90.81 c = 72.935 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 2023-09-05 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 1.6 20.64 91.9 0.0835 5.47 2.25 29170
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 1.6 1.7 92.6 0.542 1.35 1.35
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 1.6 20.64 27760 1371 91.75 0.23803 0.23682 0.2443 0.26238 0.2707 RANDOM 22.54
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] -0.59 0.6 -0.01 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 7.268 r_dihedral_angle_2_deg 6.645 r_long_range_B_refined 6.3 r_long_range_B_other 6.299 r_scangle_other 4.45 r_mcangle_it 3.515 r_mcangle_other 3.514 r_scbond_it 2.877 r_scbond_other 2.876
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.235 r_dihedral_angle_1_deg 7.268 r_dihedral_angle_2_deg 6.645 r_long_range_B_refined 6.3 r_long_range_B_other 6.299 r_scangle_other 4.45 r_mcangle_it 3.515 r_mcangle_other 3.514 r_scbond_it 2.877 r_scbond_other 2.876 r_mcbond_it 2.357 r_mcbond_other 2.357 r_angle_refined_deg 1.489 r_angle_other_deg 0.492 r_chiral_restr 0.072 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 1864 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement APEX data reduction APEX data scaling MOLREP phasing