3OXV | pdb_00003oxv

Crystal Structure of HIV-1 I50V, A71 Protease in Complex with the protease inhibitor amprenavir.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F7A	PDB entry 1F7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	295	126mM Phosphate buffer pH 6.2, 63mM Sodium Citrate, 18-33% Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.563	α = 90
b = 63.338	β = 96.61
c = 58.613	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm				SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-ID-B	1.03	APS	14-ID-B

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	1.75	50	98	0.07	8.7	4.1		36283

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	1.75	1.81	97		0.441		4.2	3565

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	PDB entry 1F7A	1.75	31.32	36262	1809	97.87	0.1705	0.1686	0.18	0.2054	0.21	RANDOM	18.7927

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]
-1.01		-0.38	0.38		0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.801
r_dihedral_angle_4_deg	17.983
r_dihedral_angle_3_deg	11.718
r_dihedral_angle_1_deg	6.075
r_scangle_it	3.676
r_scbond_it	2.262
r_mcangle_it	1.468
r_angle_refined_deg	1.36
r_mcbond_it	0.809
r_angle_other_deg	0.793

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.801
r_dihedral_angle_4_deg	17.983
r_dihedral_angle_3_deg	11.718
r_dihedral_angle_1_deg	6.075
r_scangle_it	3.676
r_scbond_it	2.262
r_mcangle_it	1.468
r_angle_refined_deg	1.36
r_mcbond_it	0.809
r_angle_other_deg	0.793
r_mcbond_other	0.224
r_chiral_restr	0.083
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2978
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	140

Software

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

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.