4C9W

Crystal structure of NUDT1 (MTH1) with R-crizotinib


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.2M AMMONIUM SULFATE, 30%(W/V) PEG 4000, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0439.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 36.2α = 90
b = 59.96β = 90
c = 66.87γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6544.6499.80.088.24.218113
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6897.40.372.63.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ZR01.6544.641712892399.530.1520.148710.21812RANDOM16.2
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]
0.38-0.430.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.379
r_sphericity_free28.595
r_dihedral_angle_4_deg11.765
r_dihedral_angle_3_deg11.679
r_sphericity_bonded8.847
r_dihedral_angle_1_deg6.101
r_long_range_B_refined3.896
r_long_range_B_other3.717
r_scangle_other2.524
r_rigid_bond_restr2.294
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.379
r_sphericity_free28.595
r_dihedral_angle_4_deg11.765
r_dihedral_angle_3_deg11.679
r_sphericity_bonded8.847
r_dihedral_angle_1_deg6.101
r_long_range_B_refined3.896
r_long_range_B_other3.717
r_scangle_other2.524
r_rigid_bond_restr2.294
r_scbond_it2.288
r_mcangle_it2.222
r_mcangle_other2.221
r_scbond_other2.108
r_mcbond_it1.69
r_mcbond_other1.69
r_angle_refined_deg1.348
r_angle_other_deg0.726
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms1239
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing