3KFN | pdb_00003kfn

HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AZ8	HIV PR dimer generated from PDB entry 2AZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	277	0.5 M KSCN, 0.1 M MES-HCL, pH 7.0, 10% DMSO, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.95	α = 90
b = 85.57	β = 90
c = 46.49	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 315r	Rh coated flat mirror	2009-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	0.97946	SSRL	BL7-1

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	1.77	48.564	93.7	0.089	0.089	3	3.4	23368	21896			27.9

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	1.77	1.82	92.5		0.637	0.637	1.1	3.4	1574

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	HIV PR dimer generated from PDB entry 2AZ8	1.77	48.55	23368	21866	1136	92.58	0.217	0.214	0.21	0.274	0.28	RANDOM	32.903

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]
3.68			-1.94		-1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.718
r_dihedral_angle_4_deg	20.329
r_dihedral_angle_3_deg	14.318
r_dihedral_angle_1_deg	6.461
r_scangle_it	4.955
r_scbond_it	3.357
r_mcangle_it	2.217
r_angle_refined_deg	1.884
r_mcbond_it	1.346
r_chiral_restr	0.145
r_bond_refined_d	0.023
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1518
Nucleic Acid Atoms
Solvent Atoms	201
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing