2A8R | pdb_00002a8r

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

X-RAY DIFFRACTION

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	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 = 50.2	α = 90
b = 82.15	β = 90
c = 112.24	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	2004-04-14	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)	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	2.45	23.51	99.4	0.046	14.1	3.46	17716	17613

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	2.45	2.54	99.5		0.365	3.1	3.48	1727

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1U20	2.45	23	17716	17559	1739	99.38	0.227	0.222	0.23	0.263	RANDOM	63.01

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]
4.24			-0.97		-3.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.647
r_dihedral_angle_4_deg	18.663
r_dihedral_angle_3_deg	15.002
r_scangle_it	6.457
r_dihedral_angle_1_deg	5.396
r_scbond_it	5.082
r_mcangle_it	2.909
r_mcbond_it	1.969
r_angle_refined_deg	1.222
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.647
r_dihedral_angle_4_deg	18.663
r_dihedral_angle_3_deg	15.002
r_scangle_it	6.457
r_dihedral_angle_1_deg	5.396
r_scbond_it	5.082
r_mcangle_it	2.909
r_mcbond_it	1.969
r_angle_refined_deg	1.222
r_nbtor_refined	0.303
r_nbd_refined	0.211
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.075
r_bond_refined_d	0.018
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2895
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	23

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

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.