2PK6

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10033

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	100 MES pH 6.5, 500 mM NaCl, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.436	α = 90
b = 85.99	β = 90
c = 46.596	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Mirrors	2005-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.54

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	1.45	33.54	97.4	0.054	0.054	12.5	3.7		41430

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	1.45	1.5	96.3		0.806	0.806	1.73	3.6	4071

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1MSM	1.45	33.54	41398	4159	97.22	0.207	0.204	0.228	RANDOM	20.527

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]
0.14			-0.05		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.107
r_dihedral_angle_3_deg	12.245
r_dihedral_angle_4_deg	10.533
r_dihedral_angle_1_deg	5.916
r_scangle_it	3.297
r_scbond_it	2.291
r_angle_refined_deg	1.83
r_mcangle_it	1.643
r_mcbond_it	1.055
r_nbtor_refined	0.319

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.107
r_dihedral_angle_3_deg	12.245
r_dihedral_angle_4_deg	10.533
r_dihedral_angle_1_deg	5.916
r_scangle_it	3.297
r_scbond_it	2.291
r_angle_refined_deg	1.83
r_mcangle_it	1.643
r_mcbond_it	1.055
r_nbtor_refined	0.319
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.161
r_symmetry_hbond_refined	0.136
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.12
r_bond_refined_d	0.016
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1516
Nucleic Acid Atoms
Solvent Atoms	280
Heterogen Atoms	60

Software

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

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.