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Crystal structure of thymidylate synthase 1/2 from Encephalitozoon cuniculi at 2.2 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TSR PDB entry 2TSR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 290 MOLECULAR DIMENSIONS PACT SCREEN CONDITION A10: 200mM MgCl2, 100mM Na-ACETATE pH 5.0, 20% PEG 6000. ECNUA.01191.A AT 11mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.41 48.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.63 α = 90 b = 72.28 β = 90 c = 61.68 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 CCD RIGAKU SATURN 944 2009-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.2 20 98.6 0.088 19.56 6.9 16818 16581 -3 35.25
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 2.26 98.4 0.571 4.1 6.5 1216
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 (All) 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 2TSR 2.2 20 16581 16581 838 98.6 0.207 0.207 0.205 0.1994 0.246 0.2381 RANDOM 13.46
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] -1.69 -0.07 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.906 r_dihedral_angle_4_deg 21.782 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_1_deg 6.226 r_scangle_it 3.557 r_scbond_it 2.3 r_angle_refined_deg 1.475 r_mcangle_it 1.398 r_angle_other_deg 0.941 r_mcbond_it 0.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.906 r_dihedral_angle_4_deg 21.782 r_dihedral_angle_3_deg 14.693 r_dihedral_angle_1_deg 6.226 r_scangle_it 3.557 r_scbond_it 2.3 r_angle_refined_deg 1.475 r_mcangle_it 1.398 r_angle_other_deg 0.941 r_mcbond_it 0.737 r_mcbond_other 0.166 r_chiral_restr 0.097 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1968 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 1
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling