☰ Navigation Tabs
Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850
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, 100 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3.5% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.75 67.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.012 α = 90 b = 94.722 β = 90 c = 225.042 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 2022-05-09 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) 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 2.8 48.42 97.9 0.11 1 11.97 12.4 46958
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 2.8 2.9 0.083
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 2.81 48.42 44547 2431 98.47 0.19785 0.19569 0.195 0.2374 0.2352 RANDOM
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] 2.58 -0.03 -2.55
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 16.511 r_scbond_it 11.573 r_scbond_other 11.572 r_angle_refined_deg 1.819 r_angle_other_deg 1.408 r_chiral_restr 0.099 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_scangle_other 16.511 r_scbond_it 11.573 r_scbond_other 11.572 r_angle_refined_deg 1.819 r_angle_other_deg 1.408 r_chiral_restr 0.099 r_gen_planes_refined 0.011 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 8438 Solvent Atoms 11 Heterogen Atoms 115
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing