☰ Navigation Tabs
Structure of Oceanobacillus iheyensis group II intron in the presence of Li+, Mg2+, and ARN25850
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 303.15 100 mM Mg-Acetate, 200 mM KCl, 50 mM LiCl, 50 mM Na-HEPES pH 7.0, 4% PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.7 66.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.888 α = 90 b = 95.155 β = 90 c = 223.768 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 2023-12-05 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 3.73 49.03 99.68 1 16.15 13.3 20343
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 3.735 3.868 0.602
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 3.73 49.03 19355 988 99.75 0.17433 0.17078 0.1705 0.2427 0.2357 RANDOM 158.905
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] 5.1 -11.77 6.68
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.584 r_long_range_B_other 20.584 r_scangle_other 16.496 r_scbond_it 10.801 r_scbond_other 10.801 r_angle_refined_deg 2.1 r_angle_other_deg 0.628 r_chiral_restr 0.073 r_gen_planes_refined 0.009 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 20.584 r_long_range_B_other 20.584 r_scangle_other 16.496 r_scbond_it 10.801 r_scbond_other 10.801 r_angle_refined_deg 2.1 r_angle_other_deg 0.628 r_chiral_restr 0.073 r_gen_planes_refined 0.009 r_bond_refined_d 0.006 r_bond_other_d 0.003 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 8416 Solvent Atoms 61 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing