3HPH

Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	291	0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.87	α = 90
b = 83.15	β = 101.96
c = 115.3	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		2008-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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	2.64	40	99.5	0.102	8.1	3.4	56209	55918	-3	-3	50.579

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	2.64	2.71	99.4		0.586	2.1	3.3	4115

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	PDB ENTRY 3HPG and 2B4J	2.64	39.01	56171	55918	2827	99.55	0.228	0.226	0.253	RANDOM	26.532

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]
0.99		2.19	-1.45		1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.431
r_dihedral_angle_4_deg	22.003
r_dihedral_angle_3_deg	17.727
r_dihedral_angle_1_deg	6.308
r_scangle_it	3.794
r_scbond_it	2.135
r_mcangle_it	1.564
r_angle_refined_deg	1.406
r_mcbond_it	0.801
r_chiral_restr	0.094

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.431
r_dihedral_angle_4_deg	22.003
r_dihedral_angle_3_deg	17.727
r_dihedral_angle_1_deg	6.308
r_scangle_it	3.794
r_scbond_it	2.135
r_mcangle_it	1.564
r_angle_refined_deg	1.406
r_mcbond_it	0.801
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8625
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	43

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
MOLREP	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.