3EKV

Crystal structure of the wild type HIV-1 protease with the inhibitor, Amprenavir

X-RAY DIFFRACTION

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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	300	126mM Sodium Phosphate pH 6.2; 63mM sodium citrate; 24-29% ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.723	α = 90
b = 57.401	β = 90
c = 61.741	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	200	IMAGE PLATE	RIGAKU RAXIS IV	Yale mirrors		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	79.7	0.029	0.029	19	3.3		14987

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1F7A	1.75	39.19	14213	756	79.78	0.19	0.19	0.18979	0.2261	RANDOM	20.564

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]
-1.67			2.02		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.17
r_dihedral_angle_4_deg	18.365
r_dihedral_angle_3_deg	13.624
r_dihedral_angle_1_deg	6.682
r_scangle_it	2.186
r_scbond_it	1.568
r_angle_refined_deg	1.414
r_mcangle_it	0.917
r_mcbond_it	0.775
r_angle_other_deg	0.753
r_symmetry_hbond_refined	0.297
r_nbd_refined	0.184
r_nbd_other	0.182
r_mcbond_other	0.18
r_nbtor_refined	0.167
r_symmetry_vdw_other	0.163
r_xyhbond_nbd_refined	0.136
r_symmetry_vdw_refined	0.129
r_chiral_restr	0.086
r_nbtor_other	0.083
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1490
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing