6Y5Z

Structure of apo Human Polyomavirus 12 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, HANGING DROP	7	293	Tacsimate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.223	α = 90
b = 136.416	β = 109.565
c = 85.379	γ = 90

Symmetry
Space Group	P 1 21 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		2012-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.07	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	1.549	44.05	95.31	0.056	0.999	16.44	3.8		181696			16.35

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	1.549	1.64			0.456	0.855	2.89

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	1.549	44.047	181695	3634	95.103	0.143	0.1427	0.1692	17.014

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]
-0.174		0.067	-0.199		0.259

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.24
r_dihedral_angle_4_deg	19.238
r_dihedral_angle_3_deg	11.29
r_dihedral_angle_1_deg	6.826
r_lrange_it	4.494
r_lrange_other	4.494
r_scangle_it	2.654
r_scangle_other	2.653
r_mcangle_it	1.869
r_mcangle_other	1.869
r_scbond_it	1.759
r_scbond_other	1.759
r_angle_refined_deg	1.548
r_angle_other_deg	1.421
r_mcbond_it	1.209
r_mcbond_other	1.203
r_symmetry_nbd_refined	0.358
r_nbd_refined	0.205
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.157
r_xyhbond_nbd_refined	0.148
r_nbd_other	0.127
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.075
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10154
Nucleic Acid Atoms
Solvent Atoms	1539
Heterogen Atoms	84

Software

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