3HPG | pdb_00003hpg

Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B4J	PDB ENTRY 2B4J and 1K6Y
experimental model	PDB	1K6Y	PDB ENTRY 2B4J and 1K6Y

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	291	25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.104	α = 90
b = 148.904	β = 113.41
c = 91.076	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 315		2008-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9696	Diamond	I04

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	3.28	40	99.6	0.11			34448	34296	-3	-3	65.905

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)
	3.28	3.46	99.7		0.665	2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 2B4J and 1K6Y	3.28	38.672	1.99	34183	34084	1718	99.71	0.214	0.212	0.2107	0.253	0.2497	RANDOM	97.809

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]
-5.629		-7.863	22.529		-16.9

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.823
f_angle_d	1.261
f_chiral_restr	0.084
f_bond_d	0.011
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12786
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XSCALE	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	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.