2DSB | pdb_00002dsb

Crystal structure of human ADP-ribose pyrophosphatase NUDT5

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	277	25% 2-methyl-2,4-pentanediol, 0.16M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.717	α = 90
b = 70.316	β = 100.41
c = 87.629	γ = 90

Symmetry
Space Group	P 1 21 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	MARRESEARCH		2005-01-02	M	MAD
2	1	x-ray	100	CCD	MARRESEARCH		2005-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BSRF BEAMLINE 3W1A	0.9794, 0.9797, 0.9819	BSRF	3W1A
2	SYNCHROTRON	BSRF BEAMLINE 3W1A	1.0000	BSRF	3W1A

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	2.5	50	96.3	0.07	20.1	3.5	34058	32826			58.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	81.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.5	35.55	34058	32813	1641	96.3	0.214	0.214	0.21	0.262	0.26	RANDOM	69.6

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]
-9.83		7.69	-11.04		20.87

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.3
c_angle_deg	1.3
c_improper_angle_d	0.84
c_bond_d	0.007
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	6440
Nucleic Acid Atoms
Solvent Atoms	218
Heterogen Atoms

Software

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