2EZ6

Crystal structure of Aquifex aeolicus RNase III (D44N) complexed with product of double-stranded RNA processing

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RC7	pdb entries 1RC7, 1YZ9, 1YYW, 1YYO
experimental model	PDB	1YZ9	pdb entries 1RC7, 1YZ9, 1YYW, 1YYO
experimental model	PDB	1YYW	pdb entries 1RC7, 1YZ9, 1YYW, 1YYO
experimental model	PDB	1YYO	pdb entries 1RC7, 1YZ9, 1YYW, 1YYO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2 M ammonium sulfate, 25% w/v PEG 3350 in 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.839	α = 90
b = 50.976	β = 104.47
c = 113.746	γ = 90

Symmetry
Space Group	P 1 21 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	BRUKER PROTEUM 300	mirror	2005-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-ID

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	2.05	30	90.6	0.061	13.3	2.5	40208	40208			43

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)
	2.05	2.12	55.2		0.411	1.6	1.6	2408

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entries 1RC7, 1YZ9, 1YYW, 1YYO	2.05	29.84	38707	38707	1932	86.8	0.215	0.205	0.205	0.21	0.258	0.26	RANDOM	48.8

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]
0.68		8.27	2.01		-2.7

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	16.8
c_scangle_it	6.61
c_scbond_it	5.13
c_mcangle_it	4.68
c_mcbond_it	3.66
c_angle_deg	1.1
c_improper_angle_d	0.97
c_bond_d	0.005
c_bond_d_na
c_bond_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3640
Nucleic Acid Atoms	1196
Solvent Atoms	298
Heterogen Atoms	2

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASES	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.