2O4S

Crystal Structure of HIV-1 Protease (Q7K) in Complex with Lopinavir

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	1.5 M NaCl, 100 mM citrate buffer pH 5.4-5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.707	α = 90
b = 85.417	β = 90
c = 46.233	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2004-02-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	1.008	NSLS	X4A

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	1.54	25.7	99.27	0.093	0.093	13.6	5.2		35654

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.537	1.577	91.54		0.702	0.702	3.04	3.9	2380

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.54	25.7	35654	3609	99.27	0.184	0.181	0.215	RANDOM	13.473

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]
-0.07			0.05		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.069
r_dihedral_angle_3_deg	11.261
r_dihedral_angle_4_deg	9.969
r_dihedral_angle_1_deg	6.058
r_scangle_it	3.182
r_scbond_it	2.029
r_angle_refined_deg	1.5
r_mcangle_it	1.251
r_mcbond_it	0.842
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.069
r_dihedral_angle_3_deg	11.261
r_dihedral_angle_4_deg	9.969
r_dihedral_angle_1_deg	6.058
r_scangle_it	3.182
r_scbond_it	2.029
r_angle_refined_deg	1.5
r_mcangle_it	1.251
r_mcbond_it	0.842
r_nbtor_refined	0.315
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.17
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.095
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1516
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	62

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.