6U7O

HIV-1 wild type protease with GRL-00819A, with phenyl-boronic-acid as P2'-ligand and with a 6-5-5-ring fused crown-like tetrahydropyranofuran as the P2-ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NU3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	298	1.4 M sodium chloride, 0.1 M sodium acetate buffer pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.921	α = 90
b = 86.479	β = 90
c = 45.875	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	PIXEL	DECTRIS EIGER X 16M		2019-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (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	1.33	50	98.9	0.061	0.067	0.027	12.8	6		53993

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.33	1.38	94.1		0.749	0.842	0.376	0.713		4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FREE R-VALUE	3NU3	1.33	33.41	51313	2635	98.82	0.1391	0.1372	0.1772	RANDOM	18.536

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]
-2.04			-0.16		2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.567
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	11.948
r_dihedral_angle_1_deg	7.002
r_rigid_bond_restr	5.036
r_angle_refined_deg	2.331
r_angle_other_deg	1.503
r_chiral_restr	0.451
r_bond_refined_d	0.02
r_gen_planes_refined	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.567
r_dihedral_angle_4_deg	16.376
r_dihedral_angle_3_deg	11.948
r_dihedral_angle_1_deg	7.002
r_rigid_bond_restr	5.036
r_angle_refined_deg	2.331
r_angle_other_deg	1.503
r_chiral_restr	0.451
r_bond_refined_d	0.02
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	98

Software

Software
Software Name	Purpose
HKL-2000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

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.