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Crystal structure of NUDT1 (MTH1) with S-crizotinib
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, 24%(W/V) PEG 4000, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.2 α = 90 b = 60.02 β = 90 c = 67 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 2012-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.2 36.2 99.6 0.05 10.4 3.9 46209
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 1.2 1.22 99.8 0.57 2.2 4
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 3ZR0 1.2 44.71 43840 2337 99.43 0.14801 0.14629 0.1565 0.18159 0.1889 RANDOM 15.877
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] 0.29 0.11 -0.4
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.512 r_dihedral_angle_2_deg 31.209 r_dihedral_angle_4_deg 11.116 r_dihedral_angle_3_deg 10.861 r_sphericity_bonded 9.749 r_dihedral_angle_1_deg 6.282 r_long_range_B_refined 4.155 r_long_range_B_other 3.303 r_scangle_other 2.791 r_scbond_it 2.736
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.512 r_dihedral_angle_2_deg 31.209 r_dihedral_angle_4_deg 11.116 r_dihedral_angle_3_deg 10.861 r_sphericity_bonded 9.749 r_dihedral_angle_1_deg 6.282 r_long_range_B_refined 4.155 r_long_range_B_other 3.303 r_scangle_other 2.791 r_scbond_it 2.736 r_scbond_other 2.443 r_mcangle_other 1.79 r_mcangle_it 1.789 r_mcbond_it 1.69 r_mcbond_other 1.685 r_angle_refined_deg 1.32 r_rigid_bond_restr 1.164 r_angle_other_deg 0.742 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 1249 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing