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Crystal structure of the human thymidylate synthase (hTS) interface variant Q62R
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 2.0-2.2 M ammonium sulfate, 0.1 M bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 4.18 70.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.939 α = 90 b = 167.07 β = 90 c = 189.97 γ = 90
Symmetry Space Group P 21 2 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 PILATUS3 6M 2017-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96861 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.55 94.99 99.9 0.163 0.178 0.072 0.993 6.9 5.9 145044 2 26.83
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.69 99.6 0.704 0.782 0.334 0.83 2.1 5.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HVY 2.55 94.99 137694 7182 99.79 0.19948 0.19643 0.25834 0.2407 RANDOM 44.012
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] -0.24 0.24 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.608 r_dihedral_angle_4_deg 21.415 r_dihedral_angle_3_deg 19.373 r_long_range_B_refined 8.655 r_dihedral_angle_1_deg 7.798 r_mcangle_it 3.518 r_scbond_it 3.24 r_angle_refined_deg 2.167 r_mcbond_it 2.153 r_chiral_restr 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.608 r_dihedral_angle_4_deg 21.415 r_dihedral_angle_3_deg 19.373 r_long_range_B_refined 8.655 r_dihedral_angle_1_deg 7.798 r_mcangle_it 3.518 r_scbond_it 3.24 r_angle_refined_deg 2.167 r_mcbond_it 2.153 r_chiral_restr 0.148 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18544 Nucleic Acid Atoms Solvent Atoms 2430 Heterogen Atoms 377
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing