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Crystal structure of Thymidylate Synthase from Burkholderia thailandensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 Internal tracking number 225920_a2. JCSG well A2. 0.1M Ammonium Citric / Citric Acid pH 5.5, 20% w/v PEG 3,000, 25% Ethylene Glycol as Cryo. Protein ButhA.01181.a.A1 PS01191 51.93mg/ml., vapor diffusion, sitting drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.5 50.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.06 α = 90 b = 107.69 β = 98.06 c = 117.24 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r 2011-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
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 1.65 49.51 95.3 0.061 14.95 4.82 174129 166030 -3 -3 25.782
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 1.65 1.69 91.4 0.53 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1tis 1.65 49.51 2 174129 166030 8295 95.37 0.178 0.177 0.175 0.203 0.2017 RANDOM 22.469
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] 1.53 0.4 -0.15 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.003 r_dihedral_angle_4_deg 14.338 r_dihedral_angle_3_deg 11.869 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 1.506 r_angle_other_deg 0.923 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.003 r_dihedral_angle_4_deg 14.338 r_dihedral_angle_3_deg 11.869 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 1.506 r_angle_other_deg 0.923 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9470 Nucleic Acid Atoms Solvent Atoms 1162 Heterogen Atoms 63
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction