3L2R | pdb_00003l2r

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DLR	PDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA
experimental model	PDB	1EX4	PDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 158.48	α = 90
b = 158.48	β = 90
c = 124.19	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		2009-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9796	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	2.88	38.999	99.2	0.12		6.3	35972	35972	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.88	3.04	100

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3DLR; 1EX4 CHAIN A RESIDUES 223-266; 7bp B-DNA	2.88	38.999	34156	1777	98.96	0.20305	0.20202	0.21	0.22232	0.22	RANDOM	74.31

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]
1.56			1.56		-3.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.294
r_dihedral_angle_4_deg	19.042
r_dihedral_angle_3_deg	18.24
r_dihedral_angle_1_deg	6.434
r_scangle_it	2.701
r_angle_refined_deg	1.657
r_scbond_it	1.591
r_mcangle_it	1.062
r_mcbond_it	0.538
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
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	4150
Nucleic Acid Atoms	732
Solvent Atoms	12
Heterogen Atoms	34

Software

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