2VBE | pdb_00002vbe

Tailspike protein of bacteriophage Sf6

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	VAPOR DIFFUSION HANGING DROP 20 DEG CELSIUS DROP: 3 UL RESERVOIR SNF 3 UL PROTEIN RESERVOIR: 0.1 M MES PH 6.5, 25% PEG 8000, 20 MM MNCL2 PROTEIN: 5MG/ML IN 10 MM SODIUM PHOSPHATE PH 7 CRYOCONDITION: 0.1 M MES PH 6.5, 25 % PEG 8000, 20 MM MNCL2

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.91	α = 90
b = 95.91	β = 90
c = 182.6	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC CCD	TOROIDAL MIRROR		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.98	19.5	95.6	0.05	11.1	2.2		39829

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	1.98	2.06	65.4		0.08	8	2.1

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	SAD	THROUGHOUT	NONE	1.98	19.5	39829	2101	95.7	0.119	0.117	0.1361	0.149	0.1592	RANDOM	12.19

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.012
r_scangle_it	3.297
r_scbond_it	2.103
r_angle_refined_deg	1.433
r_mcangle_it	1.239
r_angle_other_deg	0.835
r_mcbond_it	0.694
r_symmetry_vdw_other	0.317
r_nbd_other	0.259
r_symmetry_vdw_refined	0.233
r_nbd_refined	0.192
r_symmetry_hbond_refined	0.18
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.093
r_nbtor_other	0.082
r_bond_refined_d	0.015
r_gen_planes_other	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3825
Nucleic Acid Atoms
Solvent Atoms	627
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
SOLVE	phasing