3EKY | pdb_00003eky

Crystal Structure of wild-type HIV protease in complex with the inhibitor, Atazanavir

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
2.12	41.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.862	α = 90
b = 58.099	β = 90
c = 61.999	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	1.8	50	95.7	0.071	0.071	8.9	6.8		16904

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1F7A	1.8	42.41	16003	861	95.65	0.17739	0.17566	0.19	0.20857	0.22	RANDOM	17.92

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]
0.08			0.26		-0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.034
r_dihedral_angle_4_deg	14.01
r_dihedral_angle_3_deg	11.552
r_dihedral_angle_1_deg	5.896
r_scangle_it	1.53
r_angle_refined_deg	1.179
r_scbond_it	1.026
r_angle_other_deg	0.704
r_mcangle_it	0.596
r_mcbond_it	0.431
r_symmetry_vdw_refined	0.281
r_nbd_refined	0.181
r_nbd_other	0.173
r_nbtor_refined	0.164
r_symmetry_vdw_other	0.163
r_symmetry_hbond_refined	0.138
r_xyhbond_nbd_refined	0.125
r_mcbond_other	0.101
r_nbtor_other	0.077
r_chiral_restr	0.069
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1502
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	71

Software

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