3AVM | pdb_00003avm

Crystal structures of novel allosteric peptide inhibitors of HIV integrase in the LEDGF binding site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	40mM Tris pH 8.0, 250mM NaCl, 30mM MgCl2, 5mM DTT, 1.6-2.0M ammonium sulfate, 100mM sodium acetate buffer pH 5.0-5.5, vapor diffusion, sitting drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.768	α = 90
b = 70.768	β = 90
c = 67.279	γ = 120

Symmetry
Space Group	P 31

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		2009-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.96	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.88	67.3				30687	30687

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.88	61.29	30664	1547	99.98	0.1603	0.1584	0.157	0.1966	0.1951	RANDOM	28.2462

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]
0.38	0.19		0.38		-0.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.538
r_dihedral_angle_3_deg	15.308
r_dihedral_angle_4_deg	11.143
r_dihedral_angle_1_deg	5.922
r_angle_refined_deg	2.184
r_chiral_restr	0.192
r_bond_refined_d	0.028
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2450
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	58

Software

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

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.