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Crystal structure of native bovine pancreatic RNAs A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292 24-34% (NH4)2SO4, 0.1M sodium acetate buffer, super saturated NaCl
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.351 α = 90 b = 64.351 β = 90 c = 63.817 γ = 120
Symmetry Space Group P 32 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 CMOS BRUKER PHOTON 100 2022-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 VENTURE 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.85 17.84 99.9 0.99 20 3.8 13430
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 1.85 1.85 0.769 1.9
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 1EIC 1.85 17.84 12736 671 99.84 0.18441 0.18236 0.1912 0.22301 0.2313 RANDOM 22.801
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.454 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_4_deg 13.289 r_dihedral_angle_1_deg 7.104 r_long_range_B_refined 6.861 r_long_range_B_other 6.403 r_scangle_other 4.967 r_scbond_it 3.585 r_mcangle_it 3.367 r_mcangle_other 3.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.454 r_dihedral_angle_3_deg 13.812 r_dihedral_angle_4_deg 13.289 r_dihedral_angle_1_deg 7.104 r_long_range_B_refined 6.861 r_long_range_B_other 6.403 r_scangle_other 4.967 r_scbond_it 3.585 r_mcangle_it 3.367 r_mcangle_other 3.365 r_scbond_other 3.207 r_mcbond_other 2.146 r_mcbond_it 2.145 r_angle_refined_deg 1.779 r_angle_other_deg 1.488 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 951 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing