4O5B | pdb_00004o5b

HIV-1 Integrase Catalytic Core Domain Complexed with Allosteric Inhibitor (2S)-tert-butoxy[6-(5-chloro-1H-benzimidazol-2-yl)-2,5-dimethyl-4-phenylpyridin-3-yl]ethanoic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	0.1 M Na Cacodylate, pH 6.5, 1.4 M Na Acetate, Vapor Diffusion,hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.049	α = 90
b = 72.049	β = 90
c = 66.181	γ = 120

Symmetry
Space Group	P 31 2 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	IMAGE PLATE	RIGAKU RAXIS IV++	mirrors	2013-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.541

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	2.37	62.4	99.5	0.048	24.5	5	8457	8414	3	3

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	2.37	2.41	100		0.558		5	421

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	THROUGHOUT	2.37	62.4	8387	8317	386	99.15	0.1874	0.1851	0.1848	0.233	0.2332	RANDOM	71.855

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]
0.54	0.27		0.54		-1.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.905
r_dihedral_angle_3_deg	20.129
r_dihedral_angle_1_deg	6.597
r_mcangle_it	5.285
r_scbond_it	5.149
r_dihedral_angle_4_deg	4.231
r_mcbond_it	3.424
r_angle_refined_deg	1.871
r_chiral_restr	0.117
r_bond_refined_d	0.016

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.905
r_dihedral_angle_3_deg	20.129
r_dihedral_angle_1_deg	6.597
r_mcangle_it	5.285
r_scbond_it	5.149
r_dihedral_angle_4_deg	4.231
r_mcbond_it	3.424
r_angle_refined_deg	1.871
r_chiral_restr	0.117
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1098
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

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.