6Q23

Crystal structure of human 1G01 Fab in complex with influenza virus neuraminidase from A/California/04/2009 (H1N1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NSS	3NSS, 5ITB, 4FQL
experimental model	PDB	5ITB	3NSS, 5ITB, 4FQL
experimental model	PDB	4FQL	3NSS, 5ITB, 4FQL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.1 M Tris, pH 8.5, 10% (v/v) glycerol, 20% (w/v) PEG300, 5% (w/v) PEG8000

Crystal Properties
Matthews coefficient	Solvent content
3.45	64.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.594	α = 90
b = 234.985	β = 106.4
c = 106.275	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 16M		2019-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.03309	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	3.27	43.3	91.9	0.18	0.12	0.952	4.5	2.7		70214			53

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.27	3.38	73.1		0.57	0.43	0.876	1.1	2.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3NSS, 5ITB, 4FQL	3.27	43.3	66845	3351	90.43	0.19841	0.1963	0.24078	RANDOM	57.757

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]
-44.99		-1.54	42.93		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.598
r_dihedral_angle_4_deg	15.762
r_dihedral_angle_3_deg	15.586
r_long_range_B_refined	14.546
r_long_range_B_other	14.546
r_mcangle_it	8.599
r_mcangle_other	8.599
r_scangle_other	7.967
r_dihedral_angle_1_deg	6.963
r_mcbond_it	5.476
r_mcbond_other	5.476
r_scbond_it	5.107
r_scbond_other	5.107
r_angle_refined_deg	1.384
r_angle_other_deg	1.342
r_chiral_restr	0.055
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
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	25420
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	121

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing