9DOJ | pdb_00009doj

Influenza A virus polymerase PA subunit endonuclease domain bound to inhibitor Compound 19a

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Unpublished structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291.15	0.1 M HEPES, pH 7.5, 1.2 M ammonium sulfate, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.796	α = 90
b = 65.736	β = 115.03
c = 66.164	γ = 90

Symmetry
Space Group	P 1 21 1

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 EIGER X 9M		2021-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0000	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.476	59.95	96.7	0.026	0.037	0.02	0.998	12.7	3.5		81810

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.476	1.501	95.9		0.362	0.494	0.259	0.858	2.2	3.7

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	1.48	59.95	78000	3810	96.73	0.12485	0.12304	0.1376	0.16214	0.1689	RANDOM	29.928

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]
-0.55		-0.47	0.57		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.479
r_dihedral_angle_4_deg	18.857
r_dihedral_angle_3_deg	14.88
r_scangle_other	7.57
r_long_range_B_refined	7.397
r_long_range_B_other	7.266
r_rigid_bond_restr	6.979
r_scbond_it	6.642
r_scbond_other	6.621
r_mcangle_it	5.677
r_mcangle_other	5.676
r_dihedral_angle_1_deg	5.607
r_mcbond_it	5.015
r_mcbond_other	5.011
r_angle_refined_deg	1.909
r_angle_other_deg	1.488
r_chiral_restr	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.014
r_bond_other_d	0.002
r_gen_planes_other	0.001
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_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3258
Nucleic Acid Atoms
Solvent Atoms	416
Heterogen Atoms	71

Software

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