3ZT0

Small molecule inhibitors of the LEDGF site of HIV type 1 integrase identified by fragment screening and structure based drug design

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NF7	PDB ENTRY 3NF7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		THE PROTEIN WAS CONCENTRATED TO 5.5MG/ML IN 40 MM TRIS PH 8.0, 250 MM NACL, 30 MM MGCL2, 5 MM DTT AND SET UP IN A 1:1 RATIO WITH 1.6 TO 2.0 M AMMONIUM SULFATE, 100 MM SODIUM ACETATE BUFFER PH 5.0 TO 5.5.

Crystal Properties
Matthews coefficient	Solvent content
2.45	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.355	α = 90
b = 71.355	β = 90
c = 67.08	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 CCD	MIRRORS	2009-07-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1		Australian Synchrotron	MX1

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	1.95	45.45	100	0.07	18.5	5.6		27877		1	25.77

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	1.95	2.06	100		0.44	3.7	5.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3NF7	1.95	45.45	26328	1398	99.55	0.20504	0.20315	0.24004	RANDOM	25.553

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]
0.44	0.22		0.44		-0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.925
r_dihedral_angle_4_deg	17.396
r_dihedral_angle_3_deg	15.33
r_dihedral_angle_1_deg	6.329
r_scangle_it	3.391
r_scbond_it	2.446
r_mcangle_it	1.839
r_angle_refined_deg	1.797
r_mcbond_it	1.247
r_nbtor_refined	0.302
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.116
r_symmetry_hbond_refined	0.069
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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	2318
Nucleic Acid Atoms
Solvent Atoms	97
Heterogen Atoms	98

Software

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