1MHK | pdb_00001mhk

Crystal Structure Analysis of a 26mer RNA molecule, representing a new RNA motif, the hook-turn

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6MER	6mer A-form RNA helix

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	292	ammonium sulfate, magnesium chloride, spermidine, tris-hydrogen chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP at 292K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.169	α = 90
b = 62.51	β = 98.76
c = 50.933	γ = 90

Symmetry
Space Group	C 1 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	193	IMAGE PLATE	RIGAKU RAXIS IIC	focusing mirrors	2001-01-31	M	SINGLE WAVELENGTH
2	1	x-ray	193	CCD	CUSTOM-MADE		2001-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418
2	SYNCHROTRON	NSLS BEAMLINE X25	0.91939	NSLS	X25

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	2.5	15	98.6	0.128	10.35	17.69		3220		1	57.5

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)
	2.5		98.7		0.342	2.55	4.59	307

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6mer A-form RNA helix	2.5	15	2	3217	3011	252	93.6	0.243	0.2391	0.27	RANDOM	55.8

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]
6.17		20.29	5.29		-11.46

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	14
c_improper_angle_d	1.46
c_angle_deg	1.08
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	548
Solvent Atoms	21
Heterogen Atoms	1

Software

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