4FMI

Merkel cell polyomavirus VP1 in complex with 3'-sialyllactosamine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M sodium cacodylate, pH 6.5, 6% w/v PEG3350, 0.3 M magnesium chloride, soaked in 20 mM 3'-sialyllactosamine, cryoprotection: 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.04	α = 93.02
b = 85.7	β = 100.41
c = 248.73	γ = 108.07

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MARMOSAIC 225 mm CCD		2010-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

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	50	89.6	0.085	8.24	2.1	440784	395073		-3

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	2.05			0.471	1.62	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	50	391137	3934	89.65	0.196	0.19559	0.23589	RANDOM	23.911

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]
-0.54	-0.11	-0.63	1.37	-0.21	-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.564
r_dihedral_angle_4_deg	17.536
r_dihedral_angle_3_deg	13.442
r_dihedral_angle_1_deg	6.031
r_scangle_it	3.866
r_scbond_it	2.648
r_mcangle_it	1.785
r_angle_refined_deg	1.111
r_mcbond_it	1.015
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	42708
Nucleic Acid Atoms
Solvent Atoms	3677
Heterogen Atoms	291

Software

Software
Software Name	Purpose
RemDAq	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling