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Crystal structure of NUDT1 (MTH1) with R-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, 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 (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 1.65 44.64 17128 923 99.53 0.152 0.14871 0.1613 0.21812 0.2239 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
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