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MTH1 in complex with TH013350
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZR0 3ZR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 30% PEG6000, 0.1M Sodium Acetate pH4.0, 0.2 M Lithium Sulfate
Crystal Properties Matthews coefficient Solvent content 2.02 39.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.045 α = 90 b = 60.482 β = 90 c = 66.021 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 2022-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.8795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 36.07 100 1 17.5 12 29204
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.774
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 3ZR0 1.4 36.07 27737 1420 99.99 0.18154 0.18001 0.1898 0.21188 0.2227 RANDOM 15.728
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] 0.53 0.01 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.066 r_dihedral_angle_3_deg 12.235 r_dihedral_angle_4_deg 10.415 r_dihedral_angle_1_deg 7.254 r_long_range_B_refined 4.695 r_long_range_B_other 4.686 r_scangle_other 3.671 r_scbond_it 2.458 r_scbond_other 2.435 r_mcangle_it 1.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.066 r_dihedral_angle_3_deg 12.235 r_dihedral_angle_4_deg 10.415 r_dihedral_angle_1_deg 7.254 r_long_range_B_refined 4.695 r_long_range_B_other 4.686 r_scangle_other 3.671 r_scbond_it 2.458 r_scbond_other 2.435 r_mcangle_it 1.996 r_mcangle_other 1.995 r_angle_refined_deg 1.792 r_angle_other_deg 1.507 r_mcbond_it 1.353 r_mcbond_other 1.349 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1254 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing