5VCK

HIV Protease (PR) with TL-3 in the active site and (Z)-N-(thiazol-2-yl)-N'-tosylcarbamimidate in the exosite

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EJK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	298	1.3M NH4SO4, pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.953	α = 90
b = 62.953	β = 90
c = 82.306	γ = 120

Symmetry
Space Group	P 61

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 1		2012-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9794	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.701	32.846	99.8	0.053	0.057	0.022	16.3	6.4		20325

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.701	1.79	98.9		1.635	1.635	1.84	0.828	0.5	4.8

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	4EJK	1.8	32.846	16309	861	99.94	0.1755	0.1735	0.2142	RANDOM	39.775

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]
0.06	0.03		0.06		-0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.421
r_sphericity_free	27.711
r_dihedral_angle_3_deg	15.153
r_dihedral_angle_4_deg	12.778
r_sphericity_bonded	8.5
r_dihedral_angle_1_deg	7.17
r_mcangle_it	2.889
r_mcbond_other	2.48
r_mcbond_it	2.479
r_angle_refined_deg	1.854

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.421
r_sphericity_free	27.711
r_dihedral_angle_3_deg	15.153
r_dihedral_angle_4_deg	12.778
r_sphericity_bonded	8.5
r_dihedral_angle_1_deg	7.17
r_mcangle_it	2.889
r_mcbond_other	2.48
r_mcbond_it	2.479
r_angle_refined_deg	1.854
r_rigid_bond_restr	1.208
r_angle_other_deg	0.992
r_chiral_restr	0.093
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1512
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	104

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
autoXDS	data reduction

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.