4JEC

Joint neutron and X-ray structure of per-deuterated HIV-1 protease in complex with clinical inhibitor amprenavir

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	290	0.1M MES, pH=6; 0.8M NaCl, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.186	α = 90
b = 87.431	β = 90
c = 46.405	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++	RIGAKU OSMIC VariMax	2012-11-01	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	MAATEL CYLINDRICAL	SET OF COLLIMATORS	2012-10-02	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54		IN-HOUSE
2	NUCLEAR REACTOR	OTHER	2.8-4.0		LADI-III

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	2	59.11	50.9	0.128						7.5	3.2		12800
2	2	40	94.9	0.074						36.3	7.1		16006

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	2	2.11		0.269						4.1	3.1
2	2	2.07		0.494						4.9	6.6

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	2.01	19.77			16681	14719	724	88.2			0.194	0.203	random	30.53
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2	20		3		12800	565	77.3		0.244	0.244	0.261	random	30.53

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
x_torsion_deg	17.2
x_torsion_deg	17.2
x_angle_deg	1
x_angle_deg	1
x_torsion_impr_deg	0.88
x_torsion_impr_deg	0.88
x_bond_d	0.008
x_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	36

Software

Software
Software Name	Purpose
nCNS	refinement
MAATEL	data collection
LAUEGEN	data reduction
LSCALE	data scaling
CNS	phasing

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.