6U7P | pdb_00006u7p

HIV-1 wild type protease with GRL-03119A, with phenyl-boronic-acid as P2'-ligand and with a hexahydro-4H-furo-pyran 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	6.2	298	1.3 M sodium chloride, 0.1 M sodium acetate pH 6.2

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.491	α = 90
b = 86.097	β = 90
c = 46.086	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	1.13	50	90.8	0.061	0.066	0.026	14.8	5.7		79649

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	1.13	1.17	50.7		0.445	0.564	0.341	0.735		2

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3NU3	1.13	34.69	75718	3888	90.79	0.1258	0.125	0.1405	RANDOM	16.059

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]
-0.24			0.39		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.356
r_dihedral_angle_4_deg	17.602
r_dihedral_angle_3_deg	10.984
r_dihedral_angle_1_deg	6.993
r_rigid_bond_restr	6.274
r_angle_refined_deg	2.517
r_angle_other_deg	1.478
r_chiral_restr	0.55
r_bond_refined_d	0.025
r_gen_planes_refined	0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.356
r_dihedral_angle_4_deg	17.602
r_dihedral_angle_3_deg	10.984
r_dihedral_angle_1_deg	6.993
r_rigid_bond_restr	6.274
r_angle_refined_deg	2.517
r_angle_other_deg	1.478
r_chiral_restr	0.55
r_bond_refined_d	0.025
r_gen_planes_refined	0.015
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	97

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.