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Crystal Structure of Human Thymidyalte Synthase M190K with Loop 181-197 stabilized in the inactive conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 2.0M AS, 0.1M Tris pH 8.5, 20mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.2 61.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.053 α = 90 b = 96.053 β = 90 c = 80.064 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2006-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.003 APS 22-BM
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 2 50 88.4 0.047 59.707 11.7 29397 26021 1
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 2 2.07 40.8 0.459 2.4 1177
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 2YPV 2 41.59 29397 25970 1321 88.4 0.2 0.198 0.1948 0.238 0.2354 RANDOM 56.7
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] 0.13 0.06 0.13 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.851 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_1_deg 7.498 r_scangle_it 4.568 r_scbond_it 3.086 r_mcangle_it 2.035 r_angle_refined_deg 1.915 r_mcbond_it 1.252 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.851 r_dihedral_angle_4_deg 20.269 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_1_deg 7.498 r_scangle_it 4.568 r_scbond_it 3.086 r_mcangle_it 2.035 r_angle_refined_deg 1.915 r_mcbond_it 1.252 r_nbtor_refined 0.315 r_nbd_refined 0.229 r_symmetry_vdw_refined 0.221 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.182 r_chiral_restr 0.152 r_bond_refined_d 0.021 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2220 Nucleic Acid Atoms Solvent Atoms 158 Heterogen Atoms 14
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection CNS phasing