5NZF | pdb_00005nzf

Complex of H275Y/I223V mutant variant of neuraminidase from H1N1 influenza virus with oseltamivir

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5NWE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	291	0.1 M HEPES pH 7.0, 7% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.654	α = 90
b = 127.217	β = 92.93
c = 96.786	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 PILATUS 6M		2016-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.745	45.18	99.2	0.096	0.114	0.996	8.97	3.36		207846		-3	23.93

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85	96.9		0.561	0.673	0.71	1.91	3.23

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	5NWE	1.75	45.18	205663	2183	99.18	0.2147	0.2143	0.22	0.2552	0.26	RANDOM	18.781

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]
0.29		-0.62			-0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.659
r_dihedral_angle_4_deg	15.783
r_dihedral_angle_3_deg	12.966
r_dihedral_angle_1_deg	7.528
r_angle_refined_deg	1.786
r_angle_other_deg	1.038
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.659
r_dihedral_angle_4_deg	15.783
r_dihedral_angle_3_deg	12.966
r_dihedral_angle_1_deg	7.528
r_angle_refined_deg	1.786
r_angle_other_deg	1.038
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11972
Nucleic Acid Atoms
Solvent Atoms	1337
Heterogen Atoms	349

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.