2A8S | pdb_00002a8s

2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and 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 = 49.998	α = 90
b = 82.553	β = 90
c = 112.16	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	2005-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	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	38.74	91.9	0.057	25.4	11.34	17738	16302			54.6

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	2.45	2.54	91.3	91.3	0.343	6.9	10.04	1737

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	38.74	17692	16269	1620	91.94	0.217	0.211	0.22	0.265	RANDOM	52.338

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]
4.5			-1.48		-3.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.92
r_dihedral_angle_4_deg	17.413
r_dihedral_angle_3_deg	15.202
r_dihedral_angle_1_deg	5.146
r_scangle_it	5.035
r_scbond_it	3.392
r_mcangle_it	2.05
r_mcbond_it	1.249
r_angle_refined_deg	1.139
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.92
r_dihedral_angle_4_deg	17.413
r_dihedral_angle_3_deg	15.202
r_dihedral_angle_1_deg	5.146
r_scangle_it	5.035
r_scbond_it	3.392
r_mcangle_it	2.05
r_mcbond_it	1.249
r_angle_refined_deg	1.139
r_nbtor_refined	0.297
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.123
r_symmetry_hbond_refined	0.086
r_chiral_restr	0.068
r_bond_refined_d	0.018
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2940
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	72

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.