Experiment: 2YHT

Crystal structure of Hfq riboregulator from E. coli (P1 space group)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Y90	PDB ENTRY 2Y90

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.4	293	CRYSTALS WERE OBTAINED BY VAPOR DIFFUSION IN 2UL SITTING DROPS. THE RESERVOIR CONTAINED 30% PEG 3350, 0.1 M NA-CITRATE PH 5.4. CRYSTALLIZATIONS WERE CARRIED OUT AT 20 DEGREES CELSIUS.

Crystal Properties
Matthews coefficient	Solvent content
1.8	30

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.2	α = 82.6
b = 61.2	β = 87.3
c = 53.1	γ = 60

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 QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.9	62	97.4	0.08	12	3.7		14455		-3	28.19

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	2.9	3	82.6		0.14	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2Y90	2.9	30.566	0.05	14073	700	96.05	0.1833	0.1809	0.1827	0.2285	0.2306	26.6

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]
-9.9152	-0.978	0.3209	-9.2556	0.9528	18.9369

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.74
f_angle_d	1.154
f_chiral_restr	0.069
f_bond_d	0.009
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6048
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing