3KFR

HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of flap

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AZ8	HIV PR dimer generated from monomer with TL-3 bound in 2AZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.8	277	0.5 M KSCN, 0.1 M MES-HCL, pH 5.8, 10% DMSO, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.72	α = 90
b = 65.57	β = 90
c = 92.36	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r	Rh coated flat mirror	2008-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97946	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.15	25.3	97.8	0.051	0.051	6.7	3.8	63048	61661			12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.18	96.6		0.8	0.8	0.9	3.9	4432

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	HIV PR dimer generated from monomer with TL-3 bound in 2AZ8	1.3	25.3	42972	2151	98	0.184	0.183	0.207	RANDOM	16.693

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]
0.09			-0.02		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.783
r_dihedral_angle_4_deg	13.812
r_dihedral_angle_3_deg	10.527
r_dihedral_angle_1_deg	6.481
r_sphericity_free	4.003
r_scangle_it	3.801
r_sphericity_bonded	3.197
r_scbond_it	2.434
r_mcangle_it	1.928
r_angle_refined_deg	1.437

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.783
r_dihedral_angle_4_deg	13.812
r_dihedral_angle_3_deg	10.527
r_dihedral_angle_1_deg	6.481
r_sphericity_free	4.003
r_scangle_it	3.801
r_sphericity_bonded	3.197
r_scbond_it	2.434
r_mcangle_it	1.928
r_angle_refined_deg	1.437
r_rigid_bond_restr	1.29
r_mcbond_it	1.182
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1520
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	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.