2YDC | pdb_00002ydc

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, soaked with GTP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		3.5		CRYSTALLIZATION: 50 MM NA-CITRATE PH 3.5 & 30 % PEG 3000, SOAKING: 50 MM NA-CITRATE PH 3.5, 35 % PEG 1500 & 20 MM GTP FOR 3 H

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.89	α = 90
b = 46.43	β = 90
c = 106.49	γ = 90

Symmetry
Space Group	P 21 21 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	MARRESEARCH MAR165	MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M)	2010-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2		MAX II	I911-2

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	25	99.9	0.08	15.66	6.9		13618		-3	34.44

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	2.05	2.1	100		1.08	2.18	6.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 2XMI	2.05	19.946	1.99	13608	681	99.99	0.2041	0.2017	0.19	0.2483	0.24	48.91

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]
3.7421			-5.8502		2.1082

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.265
f_angle_d	0.762
f_chiral_restr	0.05
f_plane_restr	0.004
f_bond_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1688
Nucleic Acid Atoms
Solvent Atoms	78
Heterogen Atoms	28

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	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.