2DSD | pdb_00002dsd

Crystal structure of human ADP-ribose pyrophosphatase NUDT5 in complex with magnesium and AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DSB	PDB ENTRY 2DSB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	30% PEG 4000, 0.2M sodium acetate, 0.1M tris hydrochloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.05	39.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.076	α = 90
b = 40.156	β = 121.68
c = 100.124	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 4		2006-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0000	Photon Factory	BL-6A

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	2.6	50	97.5	0.119	18.7	5.2	12474	12038			52.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.6	2.69	87

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 (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2DSB	2.6	37.01	12474	11735	600	97.9	0.215	0.215	0.21	0.275	0.27	RANDOM	62.4

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]
-7.78		1.65	12.4		-4.61

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	25.1
c_angle_deg	1.4
c_improper_angle_d	0.87
c_bond_d	0.008
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_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3032
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	52

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing