8DCI | pdb_00008dci

Crystal Structure of a highly resistant HIV-1 protease Clinical isolate PR10x (inhibitor-free)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7L3S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	Hanging-drop vapor diffusion using equal volumes of protein stock (3.9 mg/mL) and well reservoir solution. Cryoprotected in 30% glycerol. Crystallized in 0.85 M NaCl and 0.1 M sodium acetate pH 5.4

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.366	α = 90
b = 81.351	β = 90
c = 85.615	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	100	PIXEL	DECTRIS EIGER X 16M		2018-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1	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	1.62	50	97.9	0.075	0.082	0.034	16.5	5.8		25357

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	1.62	1.68	95		0.476	0.528	0.224	0.895		5.3

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7L3S	1.62	29.5	24067	1232	97.41	0.1904	0.1887	0.2	0.2265	0.23	RANDOM	26

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]
-0.01			0.03		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.854
r_dihedral_angle_4_deg	14.345
r_dihedral_angle_3_deg	12.305
r_dihedral_angle_1_deg	7.699
r_angle_refined_deg	1.714
r_angle_other_deg	1.349
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.854
r_dihedral_angle_4_deg	14.345
r_dihedral_angle_3_deg	12.305
r_dihedral_angle_1_deg	7.699
r_angle_refined_deg	1.714
r_angle_other_deg	1.349
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1522
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms

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.