4L1A

Crystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	298	The hanging drop vapor diffusion method was used to form the bipyramidal crystals of the MDR 769 protease. Using a grid screen consisting of sodium chloride (0.7 to 1.4 M) and MES-HEPES buffer (pH 5.5 to 8.1), the HIV-1 protease substrate complex crystals formed overnight at 22 C. Routinely, 0.2 mm crystals, in the longest dimension, were obtained after 14 days of incubation. In each well, there were two droplets, containing 1 lL of protease substrate mixture, 1 lL of reservoir solution and 2 lL of protease substrate mixture, 1 lL of reservoir solution, respectively, 07 mL of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.828	α = 90
b = 43.828	β = 90
c = 101.805	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARMOSAIC 300 mm CCD		2008-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00	APS	21-ID-D

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	1.9	43.81					14375

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	43.81	14375	765	99.92	0.2006	0.19748	0.26003	RANDOM	21.672

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]
0.4			0.4		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.495
r_dihedral_angle_3_deg	14.462
r_dihedral_angle_4_deg	9.836
r_dihedral_angle_1_deg	6.065
r_scangle_it	3.738
r_scbond_it	2.284
r_angle_refined_deg	1.815
r_mcangle_it	1.699
r_mcbond_it	0.995
r_nbtor_refined	0.338

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.495
r_dihedral_angle_3_deg	14.462
r_dihedral_angle_4_deg	9.836
r_dihedral_angle_1_deg	6.065
r_scangle_it	3.738
r_scbond_it	2.284
r_angle_refined_deg	1.815
r_mcangle_it	1.699
r_mcbond_it	0.995
r_nbtor_refined	0.338
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.183
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1514
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	46

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling

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.