3EM3 | pdb_00003em3

Crystal structure of amprenavir (APV) in complex with a drug resistant HIV-1 protease variant (I50L/A71V).

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	300	pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.16	α = 90
b = 57.907	β = 90
c = 61.21	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	2004-03-17	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)	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	2.2	50	99	0.118	12.95	4.5		9644

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	2.2	2.28	95.2		0.439			910

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		THROUGHOUT	1F7A	2.2	41.89	9283	439	95.83	0.188	0.186	0.2	0.247	0.26	RANDOM	36.111

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]
-1.26			-0.58		1.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.911
r_dihedral_angle_4_deg	18.489
r_dihedral_angle_3_deg	15.074
r_dihedral_angle_1_deg	7.564
r_scangle_it	2.287
r_scbond_it	1.614
r_angle_refined_deg	1.353
r_mcangle_it	0.945
r_mcbond_it	0.765
r_angle_other_deg	0.69
r_symmetry_hbond_refined	0.351
r_symmetry_vdw_other	0.206
r_nbd_refined	0.199
r_nbd_other	0.198
r_mcbond_other	0.178
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.156
r_symmetry_vdw_refined	0.132
r_nbtor_other	0.09
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1458
Nucleic Acid Atoms
Solvent Atoms	86
Heterogen Atoms	51

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing