6Y66

Structure of Goose Hemorrhagic Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	Na formate, ammonium acetate, Na citrate tribasic, Na oxamate, Na K tartrate, MES, imidazole, PEG 8000, ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.46	α = 94.232
b = 90.54	β = 98.09
c = 101.22	γ = 107.867

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	PIXEL	DECTRIS PILATUS 2M-F		2017-01-30	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	1.95	49.58	97.71	0.1468	0.993	9.38	3.6		206886			18.43

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	1.95	2.02			0.7611	0.701	2.02

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	1.95	49.577	206888	2069	97.724	0.166	0.1652	0.2008	17.311

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]
0.879	-0.053	-1.35	0.141	-1.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.982
r_dihedral_angle_4_deg	18.975
r_dihedral_angle_3_deg	11.479
r_dihedral_angle_1_deg	7.652
r_lrange_it	4.643
r_lrange_other	4.643
r_scangle_it	2.67
r_scangle_other	2.67
r_mcangle_it	2.002
r_mcangle_other	2.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.982
r_dihedral_angle_4_deg	18.975
r_dihedral_angle_3_deg	11.479
r_dihedral_angle_1_deg	7.652
r_lrange_it	4.643
r_lrange_other	4.643
r_scangle_it	2.67
r_scangle_other	2.67
r_mcangle_it	2.002
r_mcangle_other	2.002
r_scbond_it	1.773
r_scbond_other	1.773
r_angle_refined_deg	1.467
r_angle_other_deg	1.333
r_mcbond_it	1.321
r_mcbond_other	1.32
r_nbd_other	0.308
r_symmetry_nbd_refined	0.276
r_symmetry_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.187
r_nbd_refined	0.186
r_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.159
r_symmetry_xyhbond_nbd_other	0.155
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.068
r_ncsr_local_group_25	0.053
r_ncsr_local_group_21	0.051
r_ncsr_local_group_27	0.05
r_ncsr_local_group_34	0.049
r_ncsr_local_group_35	0.049
r_ncsr_local_group_6	0.048
r_ncsr_local_group_11	0.047
r_ncsr_local_group_15	0.047
r_ncsr_local_group_28	0.047
r_ncsr_local_group_33	0.047
r_ncsr_local_group_18	0.046
r_ncsr_local_group_4	0.045
r_ncsr_local_group_17	0.045
r_ncsr_local_group_2	0.044
r_ncsr_local_group_7	0.044
r_ncsr_local_group_23	0.044
r_ncsr_local_group_24	0.044
r_ncsr_local_group_30	0.044
r_ncsr_local_group_20	0.043
r_ncsr_local_group_22	0.043
r_ncsr_local_group_32	0.043
r_ncsr_local_group_37	0.043
r_ncsr_local_group_3	0.042
r_ncsr_local_group_10	0.042
r_ncsr_local_group_14	0.042
r_ncsr_local_group_19	0.042
r_ncsr_local_group_26	0.042
r_ncsr_local_group_31	0.042
r_ncsr_local_group_40	0.042
r_ncsr_local_group_36	0.041
r_ncsr_local_group_41	0.041
r_ncsr_local_group_42	0.041
r_ncsr_local_group_1	0.04
r_ncsr_local_group_9	0.04
r_ncsr_local_group_16	0.04
r_ncsr_local_group_44	0.039
r_ncsr_local_group_45	0.039
r_ncsr_local_group_29	0.038
r_ncsr_local_group_13	0.037
r_ncsr_local_group_39	0.036
r_ncsr_local_group_43	0.036
r_ncsr_local_group_8	0.034
r_ncsr_local_group_12	0.031
r_ncsr_local_group_38	0.031
r_ncsr_local_group_5	0.03
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001