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Crystal structure of mutant V45A 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 2.91 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.281 α = 90 b = 81.281 β = 90 c = 105.24 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 RAYONIX MX300HE 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) 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 1.6 30 99.9 0.043 0.049 0.023 0.999 34.73 4.6 53607
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 1.6 1.66 0.485 0.552 0.259 0.809 3.61 4.6
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 1.6 23.754 53565 2722 99.814 0.172 0.1709 0.181 0.1894 0.1985 22.215
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] 0.129 0.065 0.129 -0.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.531 r_dihedral_angle_4_deg 17.941 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_1_deg 6.327 r_lrange_it 5.116 r_lrange_other 5.03 r_scangle_it 2.798 r_scangle_other 2.798 r_mcangle_it 2.157 r_mcangle_other 2.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.531 r_dihedral_angle_4_deg 17.941 r_dihedral_angle_3_deg 11.472 r_dihedral_angle_1_deg 6.327 r_lrange_it 5.116 r_lrange_other 5.03 r_scangle_it 2.798 r_scangle_other 2.798 r_mcangle_it 2.157 r_mcangle_other 2.156 r_scbond_it 1.736 r_scbond_other 1.735 r_angle_other_deg 1.346 r_mcbond_it 1.309 r_angle_refined_deg 1.306 r_mcbond_other 1.304 r_xyhbond_nbd_refined 0.249 r_nbd_refined 0.229 r_nbd_other 0.223 r_symmetry_xyhbond_nbd_other 0.214 r_symmetry_xyhbond_nbd_refined 0.205 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.163 r_symmetry_nbd_refined 0.148 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.061 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2296 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing