6Y61 | pdb_00006y61

Structure of apo Sheep 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		293	KSCN, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.43	α = 90
b = 130.43	β = 90
c = 221.77	γ = 120

Symmetry
Space Group	P 31

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		2016-08-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0	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	2.45	49.77	94.81	0.086	0.998	21.58	8.3		147085

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	2.45	2.538			0.526	0.929	4.69

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4FMG	2.45	49.77	147076	7336	94.803	0.163	0.161	0.17	0.1968	0.2	28.333

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]
-18.848			-18.848		37.696

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.266
r_dihedral_angle_4_deg	21.274
r_dihedral_angle_3_deg	15.063
r_dihedral_angle_1_deg	7.975
r_lrange_it	4.738
r_lrange_other	4.716
r_mcangle_it	3.193
r_mcangle_other	3.193
r_scangle_it	3.026
r_scangle_other	3.026
r_mcbond_it	2.061
r_mcbond_other	2.061
r_scbond_it	1.978
r_scbond_other	1.978
r_angle_refined_deg	1.534
r_angle_other_deg	1.269
r_nbd_other	0.23
r_symmetry_nbd_other	0.193
r_nbd_refined	0.187
r_symmetry_nbd_refined	0.184
r_symmetry_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.144
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.064
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20395
Nucleic Acid Atoms
Solvent Atoms	970
Heterogen Atoms	66

Software

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