3B7E | pdb_00003b7e

Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain in complex with zanamivir

X-RAY DIFFRACTION

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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	7.3	295	20% PEG3000, pH 7.30, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.044	α = 90
b = 129.247	β = 90
c = 118.845	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	Flat mirror; single crystal Si(111) bent monochromator	2007-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97945	SSRL	BL11-1

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	1.45	50	97.6	0.096	8.5	6.8	160198	155978

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	1.45	1.49	86.3		0.527		5.6

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	PDB ENTRY 2HTY	1.45	29.71	148122	7807	97.54	0.14114	0.14014	0.15	0.16015	0.16	RANDOM	9.675

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]
-0.61			1.1		-0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.515
r_dihedral_angle_4_deg	12.932
r_dihedral_angle_3_deg	11.564
r_dihedral_angle_1_deg	7.308
r_scangle_it	4.161
r_scbond_it	3.049
r_mcangle_it	1.873
r_angle_refined_deg	1.441
r_mcbond_it	1.318
r_angle_other_deg	0.937
r_mcbond_other	0.423
r_symmetry_vdw_other	0.246
r_nbd_other	0.207
r_nbd_refined	0.199
r_nbtor_refined	0.178
r_symmetry_hbond_refined	0.153
r_xyhbond_nbd_refined	0.135
r_symmetry_vdw_refined	0.13
r_nbtor_other	0.092
r_chiral_restr	0.088
r_metal_ion_refined	0.069
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5928
Nucleic Acid Atoms
Solvent Atoms	939
Heterogen Atoms	143

Software

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