2JE4 | pdb_00002je4

Atomic-resolution crystal structure of chemically-synthesized HIV-1 protease in complex with JG-365

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7HVP	PDB ENTRY 7HVP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP			well solution 0.1 M citrate, 0.2 M sodium phosphate, 30% saturated ammonium sulfate, and 10% DMSO, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.501	α = 90
b = 58.853	β = 90
c = 60.886	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	150					M	SINGLE WAVELENGTH
2	1	x-ray						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C		APS	14-BM-C
2	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-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	1.07	50	93.9	0.062	28.2	6.2		72978

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	1.07	1.11	82.8		0.332	2.9	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB ENTRY 7HVP	1.07	10	75585	3830	93.9	0.144	0.143		0.21	0.184	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
44	1379.92	1791.98

RMS Deviations
Key	Refinement Restraint Deviation
s_zero_chiral_vol	0.106
s_approx_iso_adps	0.098
s_non_zero_chiral_vol	0.087
s_similar_adp_cmpnt	0.061
s_anti_bump_dis_restr	0.043
s_angle_d	0.039
s_from_restr_planes	0.035
s_bond_d	0.016
s_rigid_bond_adp_cmpnt	0.007
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1567
Nucleic Acid Atoms
Solvent Atoms	394
Heterogen Atoms	59

Software

Software
Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	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.