4C9W

Crystal structure of NUDT1 (MTH1) with R-crizotinib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ZR0	PDB ENTRY 3ZR0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		0.2M AMMONIUM SULFATE, 30%(W/V) PEG 4000, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.2	α = 90
b = 59.96	β = 90
c = 66.87	γ = 90

Symmetry
Space Group	P 2 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	PIXEL	DECTRIS PILATUS 6M		2012-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	1.65	44.64	99.8	0.08	8.2	4.2		18113

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	1.65	1.68	97.4		0.37	2.6	3.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3ZR0	1.65	44.64	17128	923	99.53	0.152	0.14871	0.21812	RANDOM	16.2

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]
0.38			-0.43		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.379
r_sphericity_free	28.595
r_dihedral_angle_4_deg	11.765
r_dihedral_angle_3_deg	11.679
r_sphericity_bonded	8.847
r_dihedral_angle_1_deg	6.101
r_long_range_B_refined	3.896
r_long_range_B_other	3.717
r_scangle_other	2.524
r_rigid_bond_restr	2.294
r_scbond_it	2.288
r_mcangle_it	2.222
r_mcangle_other	2.221
r_scbond_other	2.108
r_mcbond_it	1.69
r_mcbond_other	1.69
r_angle_refined_deg	1.348
r_angle_other_deg	0.726
r_chiral_restr	0.074
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1239
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	51

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing