3GCA | pdb_00003gca

The structural basis for recognition of the preQ0 metabolite by an unusually small riboswitch aptamer domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	1.8 M Li2SO4, 0.10 M Na-cacodylate pH 6.0, 0.01 M Mg(SO4)2-, 5% (v/v) 1,3-propanediol and 2 mM spermine., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.93	75.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.5	α = 90
b = 110.5	β = 90
c = 59.31	γ = 120

Symmetry
Space Group	P 63 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	Quantum 315 CCD detector	Vertical focusing mirror; single crystal (Si111) bent monochromator (horizontal focusing).	2009-01-29	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.1395, 1.1407, 0.97622, 1.1395	SSRL	BL7-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.75	50	97.6	0.056	36.47	16.6		5990		-3	75

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.75	2.85	98.5		0.36	6.5	15.8	579

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.75	28.33	5990	441	93.4	0.245	0.2613	0.272	RANDOM	76

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]
-21			-21		42

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.3
c_improper_angle_d	1.99
c_angle_deg	1.5
c_bond_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	702
Solvent Atoms
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing