3CYE | pdb_00003cye

Cyrstal structure of the native 1918 H1N1 neuraminidase from a crystal with lattice-translocation defects

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	0.16 M CALCIUM ACETATE; 0.08 M CACODYLATE; 14.4% PEG8000; 20% GLYCEROL, PH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.728	α = 90
b = 138.472	β = 90
c = 117.86	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD		2006-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.00797	SSRL	BL9-2

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	1.65	50	97.3	0.093	22.2	4.2		113144

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	1.65	1.68	76.4		0.528		2.8	4405

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-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 2HTY	1.65	44.86	113058	5652	97.13	0.193	0.1859	0.231	0.223	RANDOM	14.726

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]
-1.25			2.27		-1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.45
r_dihedral_angle_3_deg	12.452
r_dihedral_angle_4_deg	11.825
r_dihedral_angle_1_deg	6.806
r_scangle_it	2.602
r_scbond_it	1.829
r_angle_refined_deg	1.323
r_mcangle_it	1.183
r_mcbond_it	0.768
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.45
r_dihedral_angle_3_deg	12.452
r_dihedral_angle_4_deg	11.825
r_dihedral_angle_1_deg	6.806
r_scangle_it	2.602
r_scbond_it	1.829
r_angle_refined_deg	1.323
r_mcangle_it	1.183
r_mcbond_it	0.768
r_nbtor_refined	0.301
r_nbd_refined	0.222
r_symmetry_vdw_refined	0.184
r_symmetry_hbond_refined	0.16
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.09
r_metal_ion_refined	0.089
r_bond_refined_d	0.012
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5926
Nucleic Acid Atoms
Solvent Atoms	754
Heterogen Atoms	154

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.