5VEA | pdb_00005vea

HIV Protease (PR) with TL-3 in active site and 4-methylbenzene-1,2-diamine in exosite

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.8	298	0.5M KSCN, 0.1 M MES-HCl pH 5.8, 10% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.763	α = 90
b = 62.763	β = 90
c = 82.238	γ = 120

Symmetry
Space Group	P 61 2 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 315r		2008-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.9794	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2	32.793	100	0.097	0.097	0.103	0.033	14.6	9.4		6945

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	2	2.05	100		0.67	0.67	0.709	0.226	1	9.8

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2AZ8	2	31.39	6578	328	100	0.2178	0.2148	0.21	0.2799	0.28	RANDOM	33.439

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	0.01		0.02		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.25
r_dihedral_angle_3_deg	17.103
r_dihedral_angle_4_deg	15.719
r_dihedral_angle_1_deg	7.061
r_angle_refined_deg	2.195
r_symmetry_vdw_refined	0.357
r_nbtor_refined	0.319
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.277
r_xyhbond_nbd_refined	0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.25
r_dihedral_angle_3_deg	17.103
r_dihedral_angle_4_deg	15.719
r_dihedral_angle_1_deg	7.061
r_angle_refined_deg	2.195
r_symmetry_vdw_refined	0.357
r_nbtor_refined	0.319
r_symmetry_hbond_refined	0.296
r_nbd_refined	0.277
r_xyhbond_nbd_refined	0.23
r_chiral_restr	0.148
r_bond_refined_d	0.027
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	759
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	54

Software

Software
Software Name	Purpose
MOSFLM	data collection
SCALA	data scaling
MOLREP	data processing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	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.