2X6S

Human foamy virus integrase - catalytic core. Magnesium-bound structure.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2X74	PDB ENTRY 2X74

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				1.8-2M AMMONIUM FORMATE, 100MM HEPES, PH 7.5 5MM MGCL2, 10-15% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.64	40.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.35	α = 90
b = 89.19	β = 90
c = 177.23	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	180	CCD	ADSC QUANTUM 315r	TOROIDAL FOCUSING MIRROR	2008-10-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.29	44.59	97.4	0.07	15.9	4.5		59482

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	2.29	2.41	89.3		0.54	2	2.9

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 ENTRY 2X74	2.29	44.6	56404	3009	97.23	0.22757	0.22485	0.22	0.27807	0.27	RANDOM	48.333

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]
3.3			-2.86		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.209
r_dihedral_angle_4_deg	19.375
r_dihedral_angle_3_deg	18.891
r_dihedral_angle_1_deg	5.467
r_scangle_it	2.828
r_mcangle_it	1.953
r_scbond_it	1.813
r_angle_refined_deg	1.192
r_mcbond_it	1.083
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8689
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing