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DTD from Plasmodium falciparum in complex with D-Lysine
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 1500, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.905 α = 74.8 b = 53.238 β = 75.45 c = 91.092 γ = 86.07
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2008-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.21 50 94.7 0.042 13.3 2.7 43292
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) 2.21 2.29 81.4 0.465 2.5 3710
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) 2.21 50 43289 2181 95.33 0.226 0.222 0.2208 0.29 0.2856 RANDOM 60.5
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] -1.89 0.98 -2.11 -1.25 3.22 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.439 r_dihedral_angle_3_deg 18.656 r_dihedral_angle_4_deg 18.098 r_dihedral_angle_1_deg 6.464 r_scangle_it 1.868 r_angle_refined_deg 1.23 r_mcangle_it 1.214 r_scbond_it 1.169 r_mcbond_it 0.676 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.439 r_dihedral_angle_3_deg 18.656 r_dihedral_angle_4_deg 18.098 r_dihedral_angle_1_deg 6.464 r_scangle_it 1.868 r_angle_refined_deg 1.23 r_mcangle_it 1.214 r_scbond_it 1.169 r_mcbond_it 0.676 r_nbtor_refined 0.309 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.161 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7466 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 10
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction