3BEQ | pdb_00003beq

Neuraminidase of A/Brevig Mission/1/1918 H1N1 strain

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	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	Flat collimating mirror, toroid focusing mirror	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	1.64	50	97.3	0.093	9.1	4.2	116395	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	1.64	1.68	76.4		0.528		2.8

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	1.64	44.86	107399	5652	97.13	0.18183	0.18031	0.18	0.21045	0.21	RANDOM	19.142

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]
-1.41			2.57		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.096
r_dihedral_angle_3_deg	11.974
r_dihedral_angle_4_deg	10.475
r_dihedral_angle_1_deg	7.042
r_scangle_it	5.354
r_scbond_it	3.776
r_mcangle_it	2.475
r_mcbond_it	1.556
r_angle_refined_deg	1.436
r_symmetry_vdw_other	0.212
r_nbd_other	0.202
r_nbd_refined	0.199
r_mcbond_other	0.189
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.168
r_symmetry_vdw_refined	0.158
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.102
r_nbtor_other	0.093
r_metal_ion_refined	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_bond_other_d
r_angle_other_deg
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	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