3B5F | pdb_00003b5f

Crystal Structure of a Minimally Hinged Hairpin Ribozyme Incorporating the Ade38Dap Mutation and a 2',5' Phosphodiester Linkage at the Active Site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.34	78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.49	α = 90
b = 93.49	β = 90
c = 133.82	γ = 120

Symmetry
Space Group	P 61 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	ADSC QUANTUM 270	BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING	2007-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.918	CHESS	F1

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	2.7	40.48	99.4	0.05	23.8	7.8	10109	9960			79.6

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)
	2.7	2.8	99.9		0.459	3	6.1	962

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2P7F	2.7	38.32	-3	10019	9930	921	99.1	0.224	0.223	0.21	0.25	0.23	RANDOM	81.2

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]
-5.89	-10.09		-5.89		11.79

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.2
c_improper_angle_d	1.64
c_angle_deg	1.5
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1327
Solvent Atoms	3
Heterogen Atoms	14

Software

Software
Software Name	Purpose
Adxv	data processing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
CNS	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.