2A8Q

2.6 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-GDP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	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 = 49.828	α = 90
b = 82.284	β = 90
c = 111.86	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	IMAGE PLATE	RIGAKU RAXIS IIC	Osmic confocal optics	2004-08-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.6	29.85	99.8	0.05	0.05	8.9	6.9	14734	14707			73.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.67	99.8	99.8	0.433	0.433	1.8	6.8	1071

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-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1U20	2.6	27.6	14735	14223	1443	96.81	0.208	0.202	0.258	RANDOM	60.844

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]
3.85			-0.74		-3.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_4_deg	17.905
r_dihedral_angle_3_deg	14.413
r_scangle_it	6.405
r_dihedral_angle_1_deg	5.08
r_scbond_it	4.449
r_mcangle_it	2.773
r_mcbond_it	1.715
r_angle_refined_deg	1.161
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_4_deg	17.905
r_dihedral_angle_3_deg	14.413
r_scangle_it	6.405
r_dihedral_angle_1_deg	5.08
r_scbond_it	4.449
r_mcangle_it	2.773
r_mcbond_it	1.715
r_angle_refined_deg	1.161
r_nbtor_refined	0.302
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.15
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2900
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing
MOSFLM	data reduction

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 R01GM133198.