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Crystal structure of D-Tyr-tRNA(Tyr) deacylase from Plasmodium falciparum in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other PfDTD-iodide model (not deposited)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% PEG 3350. 0.1 MES , pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.174 α = 72.86 b = 53.005 β = 76.45 c = 90.432 γ = 88.32
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 2007-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
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 2.7 25 81.3 0.08 6.9 2.7 19638
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) 2.7 2.8 44.9 0.387 2.4 1080
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 (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 PfDTD-iodide model (not deposited) 2.7 20 19597 1013 81.12 0.214 0.21 0.2117 0.285 0.2783 RANDOM 57.401
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] 3.05 -0.53 -5.23 -4.36 0.04 3.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.347 r_dihedral_angle_4_deg 19.455 r_dihedral_angle_3_deg 18.961 r_dihedral_angle_1_deg 6.722 r_scangle_it 1.495 r_angle_refined_deg 1.283 r_mcangle_it 0.951 r_scbond_it 0.914 r_mcbond_it 0.522 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.347 r_dihedral_angle_4_deg 19.455 r_dihedral_angle_3_deg 18.961 r_dihedral_angle_1_deg 6.722 r_scangle_it 1.495 r_angle_refined_deg 1.283 r_mcangle_it 0.951 r_scbond_it 0.914 r_mcbond_it 0.522 r_nbtor_refined 0.316 r_symmetry_hbond_refined 0.311 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7458 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 81
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction