6Y9I

Structure of apo Chimpanzee Polyomavirus VP1

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, SITTING DROP	7	293	Sodium acetate trihydrate, PEG 3,350, 1,5-Diaminopentane dihydrochloride

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.41	α = 68.614
b = 82.19	β = 77.361
c = 82.66	γ = 77.488

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		2019-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00003	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	1.9	46.46	99.4	0.15	0.997	9.83	6.95		117709			32.2

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	1.9	1.95	98.9		0.135	0.57	1.61	6.8

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4FMG	1.9	46.456	117709	5886	99.592	0.173	0.1706	0.2134	28.057

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]
-0.216	-0.601	0.382	0.19	-0.499	-0.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.319
r_dihedral_angle_4_deg	17.55
r_dihedral_angle_3_deg	14
r_dihedral_angle_1_deg	7.627
r_lrange_it	5.792
r_lrange_other	5.734
r_scangle_it	4.214
r_scangle_other	4.214
r_mcangle_it	3.283
r_mcangle_other	3.283
r_scbond_it	2.873
r_scbond_other	2.873
r_mcbond_it	2.278
r_mcbond_other	2.274
r_angle_refined_deg	1.57
r_angle_other_deg	1.314
r_symmetry_nbd_refined	0.254
r_nbd_other	0.254
r_symmetry_xyhbond_nbd_refined	0.22
r_nbd_refined	0.192
r_symmetry_nbd_other	0.186
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.049
r_metal_ion_refined	0.024
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10524
Nucleic Acid Atoms
Solvent Atoms	947
Heterogen Atoms	10

Software

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