2FGU | pdb_00002fgu

X-ray crystal structure of HIV-1 Protease T80S variant in complex with the inhibitor saquinavir used to explore the role of invariant Thr80 in HIV-1 protease structure, function, and viral infectivity.

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	5.5	298	0.126 M Sodium Phosphate pH 6.2, 0.063 M Sodium Citrate, 23-24% Ammonium Sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.5	α = 90
b = 57.93	β = 90
c = 61.62	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Mirrors	2004-11-05	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	2	42.22	99.1	0.073	0.073	8.2	7	12625	12625

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	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	pdb entry 1F7A	2	42.22	12625	11977	612	99.09	0.1791	0.17911	0.1764	0.19	0.23235	0.18	RANDOM	21.948

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]
-0.73			0.52		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.207
r_dihedral_angle_4_deg	27.859
r_dihedral_angle_3_deg	12.644
r_dihedral_angle_1_deg	6.942
r_scangle_it	3.321
r_scbond_it	2.217
r_angle_refined_deg	1.613
r_mcangle_it	1.443
r_mcbond_it	1.2
r_angle_other_deg	0.679
r_mcbond_other	0.263
r_symmetry_hbond_refined	0.216
r_nbd_other	0.213
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.19
r_symmetry_vdw_other	0.177
r_nbtor_refined	0.176
r_chiral_restr	0.093
r_nbtor_other	0.092
r_xyhbond_nbd_other	0.073
r_symmetry_vdw_refined	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.004
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1462
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	74

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing