2Y3X

Catalytic domain of mouse 2',3'-cyclic nucleotide 3'- phosphodiesterase, complexed with sulfate

X-RAY DIFFRACTION

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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		50MM NA-CITRATE PH 3.5, 2.9M AMMONIUM SULFATE, 10% PEG 550 MME

Crystal Properties
Matthews coefficient	Solvent content
2.33	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.43	α = 90
b = 82.43	β = 90
c = 86.31	γ = 120

Symmetry
Space Group	P 31

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 225 mm CCD		2009-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	2.1	35	99.8	0.04	19.98	3.85		38236		-3

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	2.1	2.15	99.8		0.56	2.5	3.83

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2XMI	2.1	71.4	36254	1981	99.76	0.19162	0.18971	0.2275	RANDOM	71.987

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]
30.58			30.58		-61.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.387
r_dihedral_angle_4_deg	22.379
r_dihedral_angle_3_deg	16.349
r_dihedral_angle_1_deg	6.667
r_scangle_it	4.705
r_scbond_it	3.391
r_mcangle_it	2.609
r_mcbond_it	1.668
r_angle_refined_deg	1.554
r_angle_other_deg	1.097
r_mcbond_other	0.481
r_symmetry_hbond_refined	0.287
r_symmetry_vdw_refined	0.255
r_symmetry_vdw_other	0.249
r_nbd_refined	0.212
r_nbtor_refined	0.185
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.125
r_xyhbond_nbd_other	0.103
r_nbtor_other	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4977
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing