462D | pdb_0000462d

CRYSTAL STRUCTURE OF THE HIV-1 GENOMIC RNA DIMERIZATION INITIATION SITE

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	310	DROP: CACODYLATE 25MM PH 7.0, MGCL2 5MM, KCL 150MM, MPD 1%, SPERMINE 5MM; RESERVOIR: CACODYLATE 50MM PH 7.0, MGCL2 100MM, KCL 300MM, MPD 50%, VAPOR DIFFUSION, SITTING DROP, temperature 310K

Crystal Properties
Matthews coefficient	Solvent content
2.18	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.1	α = 90
b = 59.1	β = 90
c = 64	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	CUSTOM-MADE		1998-02-25	M	SINGLE WAVELENGTH
2	1	x-ray	120	IMAGE PLATE	MAC Science DIP-2000B	MIRRORS	1998-03-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE D2AM	1.020, 1.5418	ESRF	D2AM
2	ROTATING ANODE	ENRAF-NONIUS FR591

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
1,2	2.3	15	97.9	0.069		6.5	5842	5842			43

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)
	2.3	2.38	98.3		0.135		6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MIRAS	THROUGHOUT	2.3	10	5832	5832	745	98.5	0.211	0.211	0.21	0.212	0.21	RANDOM	44.1

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]
-0.29	-0.27		-0.29		0.59

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	8.5
c_improper_angle_d	1.54
c_angle_deg	1.3
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1048
Solvent Atoms	240
Heterogen Atoms	8

Software

Software
Software Name	Purpose
SHARP	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling