6VCE | pdb_00006vce

HIV-1 wild type protease with GRL-026-18A, a crown-like tetrahydropyranotetrahydrofuran with a bridged methylene group as a 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	1.8 M sodium chloride, 0.1 M sodium acetate pH 6.2; Starting protein concentration was 4.2 mg/mL and inhibitors were complexed at 5:1 molar ratio

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.904	α = 90
b = 86.207	β = 90
c = 46.09	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	90	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	1.18	50	93.6	0.082	0.09	0.035	12.2	5.6		72509

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	1.18	1.22	55.5		0.358	0.441	0.251	0.8		2.1

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	THROUGHOUT	3NU3	1.18	33.48	68939	3516	93.36	0.1365	0.1356	0.1553	RANDOM	15.273

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]
-1.47			-0.42		1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.984
r_dihedral_angle_4_deg	18.507
r_dihedral_angle_3_deg	11.256
r_rigid_bond_restr	7.633
r_dihedral_angle_1_deg	6.803
r_angle_refined_deg	2.559
r_angle_other_deg	1.715
r_chiral_restr	0.256
r_bond_refined_d	0.021
r_gen_planes_refined	0.013

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.984
r_dihedral_angle_4_deg	18.507
r_dihedral_angle_3_deg	11.256
r_rigid_bond_restr	7.633
r_dihedral_angle_1_deg	6.803
r_angle_refined_deg	2.559
r_angle_other_deg	1.715
r_chiral_restr	0.256
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
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	225
Heterogen Atoms	115

Software

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

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.