3OY9 | pdb_00003oy9

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with manganese at 2.55 resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L2R	PDB entry 3L2R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	1.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.97	69.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.09	α = 90
b = 160.09	β = 90
c = 123.94	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	AREA DETECTOR	ADSC		2010-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.97950	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.55	39.206	98.9	0.084	14.1	5.5		52142	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.55	2.69	99		0.931	0.931	2	5.4	7536

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-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	PDB entry 3L2R	2.55	39.21	52062	2627	98.33	0.2	0.1986	0.1973	0.19	0.2217	0.22	RANDOM	58.3457

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]
1.46			1.46		-2.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.983
r_dihedral_angle_4_deg	18.176
r_dihedral_angle_3_deg	15.897
r_dihedral_angle_1_deg	6.015
r_scangle_it	2.99
r_scbond_it	1.777
r_angle_refined_deg	1.496
r_mcangle_it	1.391
r_mcbond_it	0.725
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.983
r_dihedral_angle_4_deg	18.176
r_dihedral_angle_3_deg	15.897
r_dihedral_angle_1_deg	6.015
r_scangle_it	2.99
r_scbond_it	1.777
r_angle_refined_deg	1.496
r_mcangle_it	1.391
r_mcbond_it	0.725
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4339
Nucleic Acid Atoms	732
Solvent Atoms	274
Heterogen Atoms	39

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.