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DTD from Plasmodium falciparum in complex with D-Arginine
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 2.13 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.252 α = 106.94 b = 54.863 β = 101.63 c = 92.419 γ = 94.49
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 2008-10-13 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 2.75 30 97.3 0.053 14.1 3.9 24028
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) 2.75 2.85 94.3 0.521 3.6 2303
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) 2.75 30 24027 1218 97.35 0.205 0.201 0.2014 0.275 0.2709 RANDOM 74.366
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] 0.02 -0.74 2.46 2.08 3.77 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.666 r_dihedral_angle_4_deg 23.115 r_dihedral_angle_3_deg 19.053 r_dihedral_angle_1_deg 6.56 r_scangle_it 1.714 r_angle_refined_deg 1.282 r_mcangle_it 1.056 r_scbond_it 1.037 r_mcbond_it 0.587 r_nbtor_refined 0.314
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.666 r_dihedral_angle_4_deg 23.115 r_dihedral_angle_3_deg 19.053 r_dihedral_angle_1_deg 6.56 r_scangle_it 1.714 r_angle_refined_deg 1.282 r_mcangle_it 1.056 r_scbond_it 1.037 r_mcbond_it 0.587 r_nbtor_refined 0.314 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.207 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.159 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 7357 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction