8OLV | pdb_00008olv

Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+ and ARN25850


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4E8M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP303.15100 mM magnesium acetate, 100 mM potassium chloride, 10 mM lithium chloride, 50 mM HEPES sodium, pH 7.0, 3.5% PEG8000
Crystal Properties
Matthews coefficientSolvent content
3.7567.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.012α = 90
b = 94.722β = 90
c = 225.042γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 9M2022-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.92ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.848.4297.90.11111.9712.446958
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.90.083

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.8148.4244547243198.470.197850.195690.20.23740.24RANDOM
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
KeyRefinement Restraint Deviation
r_scangle_other16.511
r_scbond_it11.573
r_scbond_other11.572
r_angle_refined_deg1.819
r_angle_other_deg1.408
r_chiral_restr0.099
r_gen_planes_refined0.011
r_bond_refined_d0.009
r_bond_other_d0.003
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_other16.511
r_scbond_it11.573
r_scbond_other11.572
r_angle_refined_deg1.819
r_angle_other_deg1.408
r_chiral_restr0.099
r_gen_planes_refined0.011
r_bond_refined_d0.009
r_bond_other_d0.003
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms
Nucleic Acid Atoms8438
Solvent Atoms11
Heterogen Atoms115

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing