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Structure of Oceanobacillus iheyensis group II intron before the first step of splicing in the presence of K+, Ca2+ and intronistat B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FAQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 303.15 100 mM potassium acetate, 100 mM potassium chloride, 100 mM calcium chloride, 50 mM HEPES sodium, pH 7.0, 4.5% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.6 65.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.147 α = 90 b = 94.133 β = 90 c = 222.878 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 2022-04-14 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 4 48.68 97.77 0.097 1 5.8 4.6 16065
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 4 4.1 0.28
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 4 48.68 15347 714 98.58 0.22225 0.22043 0.2217 0.25804 0.2407 RANDOM 212.388
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] -12.48 14.11 -1.63
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.861 r_long_range_B_other 19.839 r_scangle_other 11.538 r_scbond_it 7.018 r_scbond_other 7.016 r_angle_refined_deg 1.826 r_angle_other_deg 0.496 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 19.861 r_long_range_B_other 19.839 r_scangle_other 11.538 r_scbond_it 7.018 r_scbond_other 7.016 r_angle_refined_deg 1.826 r_angle_other_deg 0.496 r_chiral_restr 0.063 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 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 8497 Solvent Atoms 11 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing