2A8T

2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U20	PDB ENTRY 1U20

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.68	293	4-5 mg/ml X29, 0.025M HEPES pH 7.68, 3/75% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.702	α = 90
b = 81.71	β = 90
c = 111.706	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	95	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC VARIMAX CONFOCAL OPTICS	2005-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

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	46.17	99.9	0.037	19.8	6.92		27774			57.6

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	2.18	100		0.38	4.4	6.88

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1U20	2.1	46.17	27801	27773	2757	99.9	0.217	0.212	0.264	RANDOM	59.1

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]
3.62			-0.66		-2.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.229
r_dihedral_angle_4_deg	16.798
r_dihedral_angle_3_deg	14.288
r_scangle_it	5.896
r_dihedral_angle_1_deg	4.883
r_scbond_it	4.366
r_mcangle_it	2.643
r_mcbond_it	1.799
r_angle_refined_deg	1.137
r_nbtor_refined	0.297
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.16
r_xyhbond_nbd_refined	0.128
r_symmetry_hbond_refined	0.118
r_chiral_restr	0.066
r_bond_refined_d	0.014
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2924
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	108

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
CNS	refinement
CrystalClear	data collection
CrystalClear	data reduction
d*TREK	data scaling
CNS	phasing