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Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and intronistat B
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 3.74 67.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.016 α = 90 b = 94.961 β = 90 c = 223.855 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 PILATUS 2M 2021-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 39.7 99.31 0.044 1 18.58 5.4 38577
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 3.1 0.35
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 39.69 36554 2021 99.33 0.19194 0.1892 0.24241 0.2236 RANDOM 138.89
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] 4.9 -1.29 -3.61
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.604 r_long_range_B_other 24.603 r_scangle_other 21.91 r_scbond_it 15.287 r_scbond_other 15.286 r_angle_refined_deg 2.31 r_angle_other_deg 0.63 r_chiral_restr 0.083 r_gen_planes_refined 0.013 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 24.604 r_long_range_B_other 24.603 r_scangle_other 21.91 r_scbond_it 15.287 r_scbond_other 15.286 r_angle_refined_deg 2.31 r_angle_other_deg 0.63 r_chiral_restr 0.083 r_gen_planes_refined 0.013 r_bond_refined_d 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 8341 Solvent Atoms 12 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing