8DWB | pdb_00008dwb

Neuraminidase from influenza virus A/Moscow/10/1999(H3N2) in complex with sialic acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AEP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291.15	2.0 M NH4-sulfate, 0.2 M Li-sulfate, 0.1 M Tris pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
4.03	69.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 136.217	α = 90
b = 136.217	β = 90
c = 150.155	γ = 90

Symmetry
Space Group	I 4 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 EIGER X 9M		2021-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12723	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.602	100.889	100	0.123	0.999	14.6	16		92200

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.602	1.607	100		1.065	0.913	2	13.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2AEP	1.602	100.889	92173	4566	99.957	0.17	0.1693	0.17	0.1819	0.18	17.492

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]
-0.645			-0.645		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.334
r_dihedral_angle_4_deg	13.362
r_dihedral_angle_3_deg	12.402
r_dihedral_angle_1_deg	7.771
r_lrange_it	3.773
r_scangle_it	3.671
r_scbond_it	2.6
r_angle_refined_deg	1.926
r_mcangle_it	1.647
r_mcbond_it	1.207
r_nbtor_refined	0.315
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.16
r_chiral_restr	0.148
r_xyhbond_nbd_refined	0.132
r_metal_ion_refined	0.086
r_symmetry_xyhbond_nbd_refined	0.079
r_bond_refined_d	0.014
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2996
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	137

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing