6Y65 | pdb_00006y65

Structure of apo Goose Hemorrhagic 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	6.5	293	Na nitrate, Na phosphate dibasic, ammonium sulfate, MES, imidazole, PEG 8000, ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.29	α = 94.048
b = 90.41	β = 97.898
c = 100.84	γ = 108.064

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	1.45	45.97	95.36	0.068	0.999	14.26	3.6		487522			12.8

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	1.45	1.502			0.702	0.797	2.16

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	1.45	45.97	487470	4875	95.379	0.149	0.1484	0.16	0.1703	0.18	13.236

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]
0.648	-0.208	-0.707	0.117	-0.675	-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.995
r_dihedral_angle_4_deg	19.136
r_dihedral_angle_3_deg	10.905
r_dihedral_angle_1_deg	7.581
r_lrange_it	4.578
r_lrange_other	4.578
r_scangle_it	1.847
r_scangle_other	1.847
r_angle_refined_deg	1.513
r_angle_other_deg	1.421
r_mcangle_it	1.402
r_mcangle_other	1.402
r_scbond_it	1.217
r_scbond_other	1.217
r_mcbond_it	0.862
r_mcbond_other	0.861
r_symmetry_nbd_refined	0.306
r_nbd_other	0.208
r_nbd_refined	0.195
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_other	0.148
r_symmetry_xyhbond_nbd_refined	0.119
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20009
Nucleic Acid Atoms
Solvent Atoms	3289
Heterogen Atoms	434

Software

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