5E5J

Joint X-ray/neutron structure of HIV-1 protease triple mutant (V32I,I47V,V82I) with darunavir at pH 6.0

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	NaCl, MES

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.724	α = 90
b = 87.257	β = 90
c = 46.547	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	293	IMAGE PLATE	RIGAKU RAXIS IV++	OSMIC VARIMAX	2014-08-20	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	MAATEL IMAGINE	COLLIMATORS	2014-10-13	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.540
2	NUCLEAR REACTOR	LADI/ILL	2.80 - 4.0

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.85	40	98.2	0.048						26.5	3.9		21102
2	2	27.61	83.5	0.147						5.2	5.9		13170

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.85	1.92		0.478						2.8	3.9
2	2	2.11		0.267						3.2	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	1.85	20		2.5	21426	18339	926	87.9			0.194	0.201	RANDOM	27.3
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2	40		2.5	16128	11729	564	68.8			0.217	0.245	RANDOM	27.3

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_torsion_deg	16.4
c_torsion_deg	16.4
c_angle_deg	1
c_angle_deg	1
c_torsion_impr_deg	0.85
c_torsion_impr_deg	0.85
c_bond_d	0.008
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1514
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	38

Software

Software
Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
nCNS	refinement
LAUEGEN	data reduction
LSCALE	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.