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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, 0.1M MES, pH 6.2-6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.914 α = 106.19 b = 53.166 β = 101.46 c = 91.435 γ = 91.09
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 2.09 25 97.1 0.06 7.5 2.1 52153
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) 2.1 2.18 94 0.446 1.9 5054
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) 2.09 25 50160 2545 92.93 0.208 0.204 0.2031 0.271 0.2678 RANDOM 28.69
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] 0.44 1 0.73 0.17 0.52 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.714 r_dihedral_angle_3_deg 15.427 r_dihedral_angle_4_deg 14.135 r_dihedral_angle_1_deg 5.63 r_scangle_it 1.252 r_angle_refined_deg 1.027 r_mcangle_it 0.786 r_scbond_it 0.762 r_mcbond_it 0.437 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.714 r_dihedral_angle_3_deg 15.427 r_dihedral_angle_4_deg 14.135 r_dihedral_angle_1_deg 5.63 r_scangle_it 1.252 r_angle_refined_deg 1.027 r_mcangle_it 0.786 r_scbond_it 0.762 r_mcbond_it 0.437 r_nbtor_refined 0.303 r_nbd_refined 0.175 r_symmetry_vdw_refined 0.162 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7697 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 92
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction