8RUI | pdb_00008rui

Structure of Oceanobacillus iheyensis group II intron in the presence of K+, Mg2+, 5'-exon, and intronistat B after 1h soaking

X-RAY DIFFRACTION

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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, 3.5% PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.81	67.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.785	α = 90
b = 94.981	β = 90
c = 227.099	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		2023-12-12	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)	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	3.31	49.47	94.25	0.998	13.47	5.9		28279

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	3.31	3.428			0.469

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	3.31	49.47	26835	1477	94.97	0.1772	0.17397	0.17	0.23182	0.23	RANDOM	155.976

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]
6.66			-6.37		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_other	26.174
r_long_range_B_refined	26.172
r_scangle_other	23.543
r_scbond_it	16.346
r_scbond_other	16.346
r_angle_refined_deg	2.155
r_angle_other_deg	0.617
r_chiral_restr	0.076
r_gen_planes_refined	0.009
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	8341
Solvent Atoms	40
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing