3NU9 | pdb_00003nu9

Crystal Structure of HIV-1 Protease Mutant I84V with Antiviral Drug Amprenavir

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F8G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	298	Crystal was grown by the hanging-drop vapor-diffusion method at room temperature, from a 2.2 mg/ml protein solution at pH 4.0 with 0.13M NaI, 0.1M NaOAc. The inhibitor was mixed with protease in a ratio 5:1 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.513	α = 90
b = 86.881	β = 90
c = 45.448	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	CCD	MARMOSAIC 300 mm CCD		2008-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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	1.85	50	93.2	0.097		4					19.6

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)
	1.85	1.9	76.6		0.345	2.7	3.6	1552

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2F8G	1.85	9.97	949	93.09	0.20066	0.20066	0.19884	0.21	0.23555	0.25	RANDOM	27.34

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]
0.06	0.09	-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.662
r_dihedral_angle_4_deg	13.447
r_dihedral_angle_3_deg	12.564
r_dihedral_angle_1_deg	5.959
r_scangle_it	4.302
r_scbond_it	2.522
r_angle_refined_deg	1.546
r_mcangle_it	1.456
r_mcbond_it	0.841
r_nbtor_refined	0.312
r_nbd_refined	0.192
r_xyhbond_nbd_refined	0.191
r_symmetry_vdw_refined	0.17
r_symmetry_hbond_refined	0.107
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1510
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms	65

Software

Software
Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling