Experiment: 3B5S

Minimally Hinged Hairpin Ribozyme Incorporates A38DAP Mutation and 2'-O-methyl Modification at the Active Site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	PEG 2K MME, lithium sulfate, sodium cacodylate, spermidine, cobalt hexaammine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.24	78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.5	α = 90
b = 93.5	β = 90
c = 133.42	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 210	BENT TRIANGULAR ASYMMETRIC CUT SI(111) MONOCHROMATOR (PROVIDES HORIZONTAL FOCUSSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING	2006-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	0.977	CHESS	A1

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	2.25	40.49	98.5	0.037	25.5	7.8	16976	16724			113.4

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)
1	2.25	2.35	98.1		0.476	3.5	8.8	1615

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	2OUE	2.25	40.49	-3	16976	16669	1669	98.1	0.223	0.223	0.199	0.241	0.2182	RANDOM	71.1

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]
-7.78	-6.36		-7.78		15.56

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.6
c_improper_angle_d	1.85
c_angle_deg	1.6
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1312
Solvent Atoms	33
Heterogen Atoms	19

Software

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