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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and ARN25850 after 1h soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 303.15 100 mM magnesium acetate, 200 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.82 67.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.57 α = 90 b = 95.098 β = 90 c = 227.801 γ = 90
Symmetry Space Group P 21 21 21
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 DECTRIS EIGER2 X 9M 2023-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.92 ESRF ID30B
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 3.12 49.52 98.96 0.998 11.9 13.5 35276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.12 3.236 0.316
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.12 49.52 33507 1768 99.86 0.19805 0.19604 0.23617 0.2241 RANDOM 147.217
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] -0.78 8.17 -7.39
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.565 r_long_range_B_other 15.565 r_scangle_other 11.663 r_scbond_it 8.352 r_scbond_other 8.352 r_angle_refined_deg 2.472 r_angle_other_deg 0.674 r_chiral_restr 0.089 r_gen_planes_refined 0.012 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 15.565 r_long_range_B_other 15.565 r_scangle_other 11.663 r_scbond_it 8.352 r_scbond_other 8.352 r_angle_refined_deg 2.472 r_angle_other_deg 0.674 r_chiral_restr 0.089 r_gen_planes_refined 0.012 r_bond_refined_d 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_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 Nucleic Acid Atoms 8349 Solvent Atoms 63 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing