3BWQ

Structure of free SV40 VP1 pentamer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SVA	PDB ENTRY 1SVA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		273	RESERVOIR: 0.1 M TRIS, PH 8.5, 24 % PEG3350. DROP: RESERVOIR MIXED 4:1 WITH 30 % ETHYLENE GLYCOL. THIS WAS MIXED 1:1 WITH VP1 (11 MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.04	α = 90
b = 93.66	β = 105.54
c = 120.81	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2006-09-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.3	50	86.8	0.099	6.7	4.8	73715	63985

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	2.3	2.38	52.2		0.26	1.4	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1SVA	2.3	39.78	73715	57548	6346	86.81	0.21217	0.20746	0.2542	RANDOM	39.406

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]
-3.43		-3.75	4.92		-3.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.269
r_dihedral_angle_4_deg	18.159
r_dihedral_angle_3_deg	14.83
r_dihedral_angle_1_deg	5.363
r_scangle_it	4.04
r_mcangle_it	3.718
r_scbond_it	2.906
r_mcbond_it	2.391
r_angle_refined_deg	0.748
r_nbtor_refined	0.312
r_nbd_refined	0.216
r_symmetry_vdw_refined	0.138
r_xyhbond_nbd_refined	0.136
r_symmetry_hbond_refined	0.117
r_bond_refined_d	0.005
r_chiral_restr	0.002
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	10164
Nucleic Acid Atoms
Solvent Atoms	676
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing