6Y60

Structure of Human Polyomavirus 12 VP1 in complex with 3'-Sialyllactosamine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FMG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	Ammonium acetate, Bis-Tris, 2-methyl-2,4-pentanediol

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.322	α = 90
b = 141.724	β = 90
c = 251.302	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS PILATUS 2M-F		2013-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	1.798	47.37	99.4	0.125	0.999	12.21	7.04		274251			33.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.798	1.91			1.77	0.725	1.34

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4FMG	1.798	47.37	274154	2741	99.412	0.204	0.2035	0.243	30.486

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]
1.259			1.898		-3.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.246
r_dihedral_angle_4_deg	21.357
r_dihedral_angle_3_deg	12.819
r_dihedral_angle_1_deg	7.175
r_lrange_it	5.25
r_lrange_other	5.17
r_scangle_it	3.959
r_scangle_other	3.959
r_mcangle_it	3.217
r_mcangle_other	3.217
r_scbond_it	2.787
r_scbond_other	2.787
r_mcbond_it	2.422
r_mcbond_other	2.422
r_angle_refined_deg	1.629
r_angle_other_deg	1.31
r_symmetry_xyhbond_nbd_refined	0.47
r_symmetry_nbd_refined	0.245
r_nbd_other	0.213
r_nbd_refined	0.199
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19801
Nucleic Acid Atoms
Solvent Atoms	1825
Heterogen Atoms	312

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building