4KB9

Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	1.15 M NaCl + 0.1 M Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.32	54.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.477	α = 90
b = 86.3	β = 90
c = 46.045	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 225 mm CCD		2012-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM		APS	22-BM

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	1.29	50	92.6	0.061	21.9	6.5	56283	56283			13.2

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	1.29	1.34	54.7		0.436	2	2.5	3275

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R	PDB ENTRY 3NU3	1.29	10	55418	55418	2770	93.5	0.1416	0.1394	0.1394	0.1799	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
25	1645	1741.25

RMS Deviations
Key	Refinement Restraint Deviation
s_approx_iso_adps	0.082
s_non_zero_chiral_vol	0.071
s_zero_chiral_vol	0.07
s_similar_adp_cmpnt	0.052
s_angle_d	0.032
s_from_restr_planes	0.0295
s_anti_bump_dis_restr	0.028
s_bond_d	0.013
s_rigid_bond_adp_cmpnt	0.004
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	70

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	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.