3FTG

Crystal Structure of H2Db in complex with NP366-N3A variant peptide from influenza

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	0.2M lithium sulfate, 28% PEG 3350, 0.1M sodium citrate, pH 5.6, vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.64	α = 90
b = 94.98	β = 90
c = 132.24	γ = 90

Symmetry
Space Group	I 2 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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2007-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.6	20	98.7	0.06	27.55	7.22		18264		-3	47.68

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.7	97.7		0.303	6.4	6.93	1905

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	3CPL	2.6	15	18178	1857	98.89	0.229	0.221	0.304	RANDOM	40.807

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]
-0.45			-0.17		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.413
r_dihedral_angle_3_deg	20.701
r_dihedral_angle_4_deg	19.5
r_dihedral_angle_1_deg	7.048
r_scangle_it	2.037
r_angle_refined_deg	1.468
r_scbond_it	1.346
r_mcangle_it	1.216
r_mcbond_it	0.686
r_nbtor_refined	0.308

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.413
r_dihedral_angle_3_deg	20.701
r_dihedral_angle_4_deg	19.5
r_dihedral_angle_1_deg	7.048
r_scangle_it	2.037
r_angle_refined_deg	1.468
r_scbond_it	1.346
r_mcangle_it	1.216
r_mcbond_it	0.686
r_nbtor_refined	0.308
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.231
r_symmetry_hbond_refined	0.225
r_xyhbond_nbd_refined	0.19
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2936
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms

Software

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

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 R01GM133198.