2PK5

Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I ) in Complex with KNI-10075

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	5.4	298	100 mM citrate buffer pH 5.4, NaCl 750 mM, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 298KK

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.842	α = 90
b = 85.991	β = 90
c = 46.21	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 315		2004-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.10	NSLS	X25

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	1.9	50	99.8	0.113	0.113	14.2	6		19013

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	1.9	1.97	99.9		0.415	0.415	8.63	5.9	1856

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	1.9	48.56	18976	1940	99.72	0.164	0.16	0.2	RANDOM	23.898

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]
-0.26					0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.089
r_dihedral_angle_4_deg	16.876
r_dihedral_angle_3_deg	11.633
r_dihedral_angle_1_deg	6.276
r_scangle_it	3.166
r_scbond_it	2.183
r_angle_refined_deg	1.591
r_mcangle_it	1.294
r_mcbond_it	0.952
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.089
r_dihedral_angle_4_deg	16.876
r_dihedral_angle_3_deg	11.633
r_dihedral_angle_1_deg	6.276
r_scangle_it	3.166
r_scbond_it	2.183
r_angle_refined_deg	1.591
r_mcangle_it	1.294
r_mcbond_it	0.952
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.205
r_xyhbond_nbd_refined	0.161
r_symmetry_hbond_refined	0.108
r_chiral_restr	0.102
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1516
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	62

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.