4PH1

C-terminal domain of capsid protein from bovine leukemia virus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H47	a number of search probes were generated by comparative modelling with the Rosetta suite [Das, R. & Baker, D. Macromolecular modeling with rosetta (2008) Annu Rev Biochem 77, 363-82], using PDB ID 3h47 as a template. In this way, 10000 models were obtained, scored and clustered. Several top ranking models gave solutions in MR using the program Phaser. To note, using PDB 3H47 (or any other available PDB with similar sequence) did not produce right solutions.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	0.1M Tris.HCl, 1.25M Ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
1.92	35.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.707	α = 90
b = 52.877	β = 90
c = 90.873	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2012-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	2.457	45.703	98.9	0.109	0.129	0.067	10.2	3.5	8737	8737			36.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.457	2.59	96.3		0.378	0.378	0.232	2	3.5	1194

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	a number of search probes were generated by comparative modelling with the Rosetta suite [Das, R. & Baker, D. Macromolecular modeling with rosetta (2008) Annu Rev Biochem 77, 363-82], using PDB ID 3h47 as a template. In this way, 10000 models were obtained, scored and clustered. Several top ranking models gave solutions in MR using the program Phaser. To note, using PDB 3H47 (or any other available PDB with similar sequence) did not produce right solutions.	2.46	35.42	8701	867	98.89	0.2047	0.1993	0.2533	RANDOM	33.56

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]
1.6214			5.3721		-6.9935

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	20.23
t_omega_torsion	2.55
t_angle_deg	1.21
t_bond_d	0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1723
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
XDS	data scaling
PDB_EXTRACT	data extraction
BUSTER	refinement