2X7L

Implications of the HIV-1 Rev dimer structure at 3.2A resolution for multimeric binding to the Rev response element

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JPS	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2QR0	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2R8S	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	3BDY	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	1TZH	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	1ZA3	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2R0K	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2V7N	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	3DVG	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	1B2W	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	1BEY	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	1TZI	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2FJF	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2QQN	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	1B4J	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2FGW	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	2FJH	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85
experimental model	PDB	3D85	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		12% POLYETHYLENE GLYCOL (PEG) 6000, 100 MM DI-AMMONIUM PHOSPHATE (DAP), AND 100 MM TRIS/HCL (PH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
4.11	69.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.678	α = 94.86
b = 87.692	β = 95.5
c = 176.334	γ = 104.6

Symmetry
Space Group	P 1

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 CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	3.2	48.8	99	0.12	9.9	3.4		83664			77.96

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	3.2	3.26	98.8		1	1.1	3.4

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	PDB ENTRIES 1JPS, 2QR0, 2R8S, 3BDY, 1TZH, 1ZA3, 2R0K 2V7N, 3DVG, 1B2W, 1BEY, 1TZI, 2FJF, 2QQN, 1B4J, 2FGW, 2FJH, 3D85	3.17	48.78	83636	4187		0.2346	0.2337	0.25	0.25	0.27	RANDOM	143.62

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]
-18.228	13.1177	-6.3827	-15.9372	-4.1363	34.1652

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	23.05
t_omega_torsion	2.69
t_angle_deg	1.32
t_bond_d	0.01
t_dihedral_angle_d
t_incorr_chiral_ct
t_pseud_angle
t_trig_c_planes
t_gen_planes
t_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	22554
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	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.