4EYR | pdb_00004eyr

Crystal structure of multidrug-resistant clinical isolate 769 HIV-1 protease in complex with ritonavir

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.8	295	0.8M NaCl, 0.1 M MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.398	α = 90
b = 45.398	β = 90
c = 104.071	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARMOSAIC 300 mm CCD		2008-08-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	19.927					22513

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8		18185	973	98.28	0.19327	0.19147	0.19	0.2258	RANDOM	27.028

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]
-0.03			-0.03		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.017
r_dihedral_angle_3_deg	11.754
r_dihedral_angle_4_deg	10.76
r_dihedral_angle_1_deg	5.88
r_scangle_it	4.198
r_scbond_it	2.589
r_mcangle_it	1.894
r_angle_refined_deg	1.636
r_mcbond_it	1.165
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.017
r_dihedral_angle_3_deg	11.754
r_dihedral_angle_4_deg	10.76
r_dihedral_angle_1_deg	5.88
r_scangle_it	4.198
r_scbond_it	2.589
r_mcangle_it	1.894
r_angle_refined_deg	1.636
r_mcbond_it	1.165
r_nbtor_refined	0.315
r_nbd_refined	0.243
r_symmetry_vdw_refined	0.194
r_symmetry_hbond_refined	0.173
r_xyhbond_nbd_refined	0.166
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1514
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	50

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.