2XSQ

Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3COU	PDB ENTRY 3COU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN WAS MIXED WITH 5MM MGCL2 AND 2MM IDP PRIOR SETTING-UP THE PLATES. THEN IT WAS CRYSTALLIZED FROM 20MM MGCL2, 22% W/V POLYACRYLIC ACID 5100 AND 0.1M HEPES PH 7.5.

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.583	α = 90
b = 141.583	β = 90
c = 141.583	γ = 90

Symmetry
Space Group	F 2 3

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 CCD	MIRRORS	2010-07-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03		Diamond	I03

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	1.72	42.69	100	0.06	11.3	6.8		25010		-3	21.062

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	1.72	1.81	100		0.7	1.1	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 3COU	1.72	81.74	23737	1273	99.97	0.15983	0.15864	0.17	0.18145	0.19	RANDOM	15.756

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.129
r_dihedral_angle_4_deg	14.596
r_dihedral_angle_3_deg	11.184
r_dihedral_angle_1_deg	5.553
r_scangle_it	3.322
r_scbond_it	1.946
r_angle_refined_deg	1.276
r_mcangle_it	1.269
r_angle_other_deg	0.838
r_mcbond_it	0.666
r_mcbond_other	0.133
r_chiral_restr	0.067
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1393
Nucleic Acid Atoms
Solvent Atoms	236
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing