4FMG | pdb_00004fmg

Merkel Cell Polyomavirus VP1 Unassembled Pentamer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M sodium cacodylate, pH 6.5, 6% w/v PEG3350, 0.3 M magnesium chloride, cryoprotection: 25% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.27	α = 92.98
b = 85.62	β = 100.5
c = 248.17	γ = 108.05

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	CCD	RAYONIX MX-225		2009-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.1	50	92.3	0.113	8.98	2.8	380544	351188		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	64.7		0.569	1.95	2.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.1	50	347623	3543	92.31	0.18277	0.18232	0.18	0.22699	0.22	RANDOM	24.932

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]
0.78	0.55	0.05	1.13	0.09	-1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.413
r_dihedral_angle_4_deg	17.522
r_dihedral_angle_3_deg	13.805
r_dihedral_angle_1_deg	6.119
r_scangle_it	3.978
r_scbond_it	2.751
r_mcangle_it	1.817
r_angle_refined_deg	1.104
r_mcbond_it	1.002
r_chiral_restr	0.074
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	42369
Nucleic Acid Atoms
Solvent Atoms	3274
Heterogen Atoms	212

Software

Software
Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling