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Crystal structure of wild type Brugia malayi thymidylate synthase complexed with 2'-deoxyuridine monophosphate and methotrexate
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 7.5 273 0.1 M HEPES, pH 7.5, 0.9 M sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.434 α = 90 b = 81.434 β = 90 c = 105.37 γ = 120
Symmetry Space Group P 32 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 110 CCD MARMOSAIC 300 mm CCD DCM 2013-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 30 99.7 0.049 0.06 0.033 26.06 5.4 65291
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 1.5 1.55 100 0.491 0.597 0.331 0.718 3.16 5.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1HVY 1.5 25.855 65249 3311 99.5 0.178 0.1767 0.1854 0.1914 0.1985 25.565
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] 0.233 0.117 0.233 -0.757
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.262 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 11.441 r_dihedral_angle_1_deg 6.459 r_lrange_it 5.202 r_lrange_other 5.023 r_scangle_it 2.882 r_scangle_other 2.881 r_mcangle_other 2.256 r_mcangle_it 2.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.262 r_dihedral_angle_4_deg 17.075 r_dihedral_angle_3_deg 11.441 r_dihedral_angle_1_deg 6.459 r_lrange_it 5.202 r_lrange_other 5.023 r_scangle_it 2.882 r_scangle_other 2.881 r_mcangle_other 2.256 r_mcangle_it 2.255 r_scbond_it 1.82 r_scbond_other 1.82 r_mcbond_it 1.384 r_mcbond_other 1.372 r_angle_other_deg 1.342 r_angle_refined_deg 1.297 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.224 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_refined 0.191 r_symmetry_nbd_other 0.188 r_nbd_other 0.188 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_other 0.097 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.06 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing