9NY9 | pdb_00009ny9

Crystal structure of the post-reactive state of porcine OAS1 in complex with dsRNA, catalytic center bound PPi, and dissociated 25A2.

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	8.3	291	50 mM Tris HCl pH 8.3, 100 mM KCl, 10 mM MgCl2, 23 % (v / v) PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.405	α = 90
b = 71.405	β = 90
c = 203.56	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 PILATUS 6M-F		2019-09-13	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	2.74	49.01	99.8	0.166	0.073	0.998	9.05	13.36		14649			60.869

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	2.74	2.84			0.739	0.494	0.946

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	2.74	49.01	14593	745	99.904	0.235	0.2341	0.2357	0.2536	0.2514	69.447

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]
3.537			3.537		-7.074

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.665
r_dihedral_angle_4_deg	21.417
r_dihedral_angle_3_deg	14.218
r_lrange_it	13.505
r_lrange_other	13.274
r_scangle_it	10.27
r_scangle_other	10.269
r_mcangle_other	9.343
r_mcangle_it	9.339
r_scbond_it	6.905
r_scbond_other	6.904
r_dihedral_angle_1_deg	6.361
r_mcbond_it	6.227
r_mcbond_other	6.196
r_angle_other_deg	2.034
r_angle_refined_deg	1.574
r_nbd_other	0.262
r_symmetry_xyhbond_nbd_refined	0.253
r_symmetry_nbd_other	0.219
r_xyhbond_nbd_refined	0.197
r_nbtor_refined	0.189
r_nbd_refined	0.177
r_chiral_restr	0.124
r_symmetry_nbd_refined	0.108
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_other	0.058
r_bond_other_d	0.032
r_bond_refined_d	0.018
r_gen_planes_other	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2834
Nucleic Acid Atoms	799
Solvent Atoms	205
Heterogen Atoms	64

Software

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