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Plasmodium falciparum thymidylate kinase in complex with AP5dT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WWF PDB ENTRY 2WWF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 2.04 M SODIUM MALONATE, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.98 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.539 α = 90 b = 109.539 β = 90 c = 119.351 γ = 120
Symmetry Space Group P 31 2 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 CCD 2007-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 40 99.2 0.12 16.8 8.1 23265
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 2.7 2.8 92.4 0.49 1.7 3.7
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 PDB ENTRY 2WWF 2.7 94.92 21882 1189 99.2 0.191 0.187 0.1865 0.27 0.2608 RANDOM 37.55
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] 1.14 0.57 1.14 -1.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.863 r_dihedral_angle_4_deg 22.38 r_dihedral_angle_3_deg 19.581 r_dihedral_angle_1_deg 6.773 r_scangle_it 3.054 r_scbond_it 1.825 r_angle_refined_deg 1.655 r_mcangle_it 1.279 r_mcbond_it 0.653 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.863 r_dihedral_angle_4_deg 22.38 r_dihedral_angle_3_deg 19.581 r_dihedral_angle_1_deg 6.773 r_scangle_it 3.054 r_scbond_it 1.825 r_angle_refined_deg 1.655 r_mcangle_it 1.279 r_mcbond_it 0.653 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5239 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing