6E4C | pdb_00006e4c

The N-terminal domain of PA endonuclease from the influenza H1N1 virus in complex with 3-hydroxy-6-(2-methyl-4-(5-oxo-4,5-dihydro-1,2,4-oxadiazol-3-yl)phenyl)-4-oxo-1,4-dihydropyridine-2-carboxylic acid

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	306	30% PEG4000, 100 mM Tris, pH 8.35, 200-220 mM sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.164	α = 90
b = 75.164	β = 90
c = 120.628	γ = 120

Symmetry
Space Group	P 62 2 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 PILATUS3 6M		2018-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.35	44.28	99.9	0.034	0.035	0.01	62.6	23.3		8894

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.44	99.6		0.456	0.475	0.13	7.5	24.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 4AWM	2.35	44.28	8198	672	99.72	0.20041	0.19541	0.21	0.26027	0.27	RANDOM	53.646

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]
-0.59	-0.29		-0.59		1.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.397
r_dihedral_angle_4_deg	21.214
r_dihedral_angle_3_deg	17.195
r_long_range_B_other	8.388
r_long_range_B_refined	8.382
r_scangle_other	7.139
r_dihedral_angle_1_deg	5.97
r_mcangle_it	5.195
r_mcangle_other	5.192
r_scbond_it	4.894
r_scbond_other	4.887
r_mcbond_it	3.672
r_mcbond_other	3.665
r_angle_refined_deg	1.348
r_angle_other_deg	0.923
r_chiral_restr	0.065
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1468
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	30

Software

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