9NYB | pdb_00009nyb

Crystal structure of the pre-reactive state of porcine OAS1 in complex with dsRNA, two ApCpp substrate analogs, three catalytic Mn2+ ions.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RWN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	291	100 mM Tris HCl pH 7.6, 33% (v / v) PEG200

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.03	α = 90
b = 72.03	β = 90
c = 206.32	γ = 90

Symmetry
Space Group	P 43 21 2

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 16M	Si-111 and Si-113 reflection	2024-06-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.6	45.712	99.9	0.056	0.019	1	23.42	26.38		72726			35.688

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.7			0.803	0.415	0.952	2.15

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.6	45.712	72613	3679	99.933	0.155	0.1525	0.1666	0.2114	0.2169	41.61

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]
0.2			0.2		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.315
r_dihedral_angle_4_deg	24.051
r_rigid_bond_restr	11.949
r_dihedral_angle_3_deg	11.941
r_dihedral_angle_1_deg	6.332
r_lrange_it	5.823
r_lrange_other	4.897
r_scangle_it	4.216
r_scangle_other	4.216
r_mcangle_other	3.453
r_mcangle_it	3.449
r_scbond_other	3.044
r_scbond_it	3.043
r_mcbond_it	2.452
r_mcbond_other	2.449
r_angle_other_deg	2.135
r_angle_refined_deg	2.033
r_symmetry_xyhbond_nbd_refined	0.25
r_xyhbond_nbd_refined	0.238
r_nbd_refined	0.232
r_symmetry_nbd_other	0.223
r_nbd_other	0.198
r_nbtor_refined	0.196
r_symmetry_nbd_refined	0.153
r_chiral_restr	0.15
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.04
r_bond_other_d	0.031
r_gen_planes_other	0.023
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2835
Nucleic Acid Atoms	799
Solvent Atoms	874
Heterogen Atoms	72

Software

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