2FGV | pdb_00002fgv

X-ray crystal structure of HIV-1 Protease T80N 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	41.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.52	α = 90
b = 58.18	β = 90
c = 61.52	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	2004-11-04	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	1.5	42.26	99.3	0.042	0.042	17.7	4.2	29647	29647

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1F7A	1.5	42.26	29647	28102	1499	99.38	0.1726	0.17265	0.17138	0.19722	RANDOM	16.077

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]
-0.33			0.17		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.026
r_dihedral_angle_4_deg	15.07
r_dihedral_angle_3_deg	10.54
r_dihedral_angle_1_deg	6.181
r_scangle_it	2.119
r_scbond_it	1.429
r_angle_refined_deg	1.376
r_mcangle_it	0.873
r_mcbond_it	0.724
r_angle_other_deg	0.717
r_symmetry_hbond_refined	0.189
r_nbd_refined	0.186
r_symmetry_vdw_other	0.177
r_nbd_other	0.174
r_nbtor_refined	0.17
r_mcbond_other	0.164
r_xyhbond_nbd_refined	0.159
r_symmetry_vdw_refined	0.113
r_chiral_restr	0.085
r_nbtor_other	0.08
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1494
Nucleic Acid Atoms
Solvent Atoms	193
Heterogen Atoms	84

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
AMoRE	phasing