4OOG | pdb_00004oog

Crystal structure of yeast RNase III (Rnt1p) complexed with the product of dsRNA processing

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RV0	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	3RV1	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	1YYW	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	2NUG	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	1O0W	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	3N3W	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	3O2R	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	3C4T	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O
experimental model	PDB	1T4O	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	25% PEG1000, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.35	63.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.972	α = 90
b = 183.804	β = 90
c = 61.289	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARMOSAIC 300 mm CCD	mirrors	2011-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	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	2.5	40	98.7	0.066	14.45	4.7		31418		-3	50.22

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)
1	2.5	2.65	97.5		0.784	1.82	4.3	4870

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 3RV0, 3RV1, 1YYW, 2NUG, 1O0W, 3N3W, 3O2R, 3C4T, AND 1T4O	2.5	39.719	1.99	31130	31130	1015	99.16	0.2168	0.216	0.22	0.2394	0.24	RANDOM	78.4156

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]
-20.7225			42.6053		-21.8827

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	14.275
f_angle_d	0.777
f_chiral_restr	0.059
f_bond_d	0.01
f_plane_restr	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3897
Nucleic Acid Atoms	725
Solvent Atoms	98
Heterogen Atoms	4

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction
PHENIX	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.