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Crystal structure of zebrafish MTH1 in complex with TH588
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZR1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 28% PEG 10K, 0.1 M Sodium acetate, pH 4.0, 0.2 M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.05 39.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.26 α = 90 b = 71.202 β = 90 c = 60.924 γ = 90
Symmetry Space Group P 21 21 2
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 2015-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91991 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.9 47.6 99.9 0.21 0.995 7.9 7.2 26840
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 1.9 1.94 100 1 2 7.1
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 3ZR1 1.9 47.6 25407 1377 99.86 0.18615 0.18357 0.1936 0.23556 0.239 RANDOM 18.274
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] 0.91 -0.54 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 18.846 r_dihedral_angle_3_deg 13.372 r_dihedral_angle_1_deg 5.981 r_long_range_B_refined 5.337 r_long_range_B_other 5.337 r_scangle_other 2.349 r_mcangle_it 1.793 r_mcangle_other 1.792 r_scbond_it 1.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 18.846 r_dihedral_angle_3_deg 13.372 r_dihedral_angle_1_deg 5.981 r_long_range_B_refined 5.337 r_long_range_B_other 5.337 r_scangle_other 2.349 r_mcangle_it 1.793 r_mcangle_other 1.792 r_scbond_it 1.406 r_scbond_other 1.406 r_angle_refined_deg 1.311 r_mcbond_it 1.042 r_mcbond_other 1.041 r_angle_other_deg 0.914 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.005 r_gen_planes_other 0.003 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2506 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing