4TVG

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment AK-2097 in the outside/top of flap

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	298	2.4M NaFormate, 10% DMSO, pH4.5 NaOAc, 1.5% b-octyl glucoside

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.548	α = 90
b = 65.273	β = 90
c = 91.503	γ = 90

Symmetry
Space Group	P 21 21 21

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	APEX II CCD		2010-12-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418 A

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	2.179	53.139	98.8	34.24	8.48		9352

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.22	80		0.43	3.9	4.1

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	4EJD	2.18	37.46	9352	450	98.81	0.1998	0.1963	0.2722	RANDOM	21.778

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]
			0.02		-0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.133
r_dihedral_angle_3_deg	14.125
r_dihedral_angle_4_deg	7.244
r_dihedral_angle_1_deg	7.092
r_mcangle_it	3.007
r_mcbond_it	1.756
r_mcbond_other	1.756
r_angle_refined_deg	1.641
r_angle_other_deg	0.847
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.133
r_dihedral_angle_3_deg	14.125
r_dihedral_angle_4_deg	7.244
r_dihedral_angle_1_deg	7.092
r_mcangle_it	3.007
r_mcbond_it	1.756
r_mcbond_other	1.756
r_angle_refined_deg	1.641
r_angle_other_deg	0.847
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1552
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	43

Software

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

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.