1ZFV | pdb_00001zfv

The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZFR	PDB ENTRY 1ZFR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 2000 MME, LITHIUM SULFATE, SPERMIDINE, COBALT HEXAAMINE , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4	69.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.51	α = 90
b = 93.51	β = 90
c = 124.55	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 FOCUSING), RH-COATED SI MIRROR FOR VERTICAL FOCUSSING	2004-11-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1		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	2.4	44	99.8	0.045	27.4	11.9		13112		-5	74.3

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)
	2.4	2.49	100		0.428	4.9	11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB ENTRY 1ZFR	2.4	43.77	-5	13112	13109	1214	99.7	0.243	0.243	0.23	0.253	0.24	RANDOM	74.9

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]
-13.47	-4.46		-13.47		26.94

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	17.6
c_scangle_it	4.28
c_mcangle_it	2.96
c_scbond_it	2.34
c_improper_angle_d	2.19
c_mcbond_it	1.71
c_angle_deg	1.5
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	1310
Solvent Atoms	34
Heterogen Atoms	12

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
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.