2A8P | pdb_00002a8p

2.7 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese

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 = 50.239	α = 90
b = 82.045	β = 90
c = 112.009	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	2004-08-26	M	SINGLE WAVELENGTH

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

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	2.7	29.97	99.9	0.051	0.051	9.6	6.9		13267			72.4

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	2.7	2.74	100		0.358	0.358	2.2	7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1U20	2.7	27.6	13276	13245	1249	99.8	0.198	0.198	0.24	0.262	RANDOM	66.71

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]
3.91			-1.11		-2.8

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	6.36
c_scbond_it	4.49
c_mcangle_it	2.89
c_mcbond_it	1.8
c_angle_deg	1.22
c_bond_d	0.02
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2913
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	4

Software

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