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Plasmodium falciparum thymidylate kinase in complex with TMP and ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E2Q PDB ENTRY 1E2Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 75 MM HEPES PH 7.5, 1.35 M TRI- SODIUM CITRATE, 0.125 M NACL
Crystal Properties Matthews coefficient Solvent content 2.98 58.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.127 α = 90 b = 110.127 β = 90 c = 120.097 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 2007-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.9 40 94.3 0.08 17.4 5.1 67190
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 1.9 1.93 47.4 0.3 2.2 2
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 1E2Q 1.89 95.35 60137 3198 94.3 0.163 0.16 0.1601 0.203 0.2012 RANDOM 19.96
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] 0.5 0.25 0.5 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_dihedral_angle_4_deg 28.989 r_dihedral_angle_3_deg 14.98 r_dihedral_angle_1_deg 5.734 r_scangle_it 5.337 r_scbond_it 3.45 r_mcangle_it 2.058 r_angle_refined_deg 2.007 r_mcbond_it 1.144 r_chiral_restr 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.298 r_dihedral_angle_4_deg 28.989 r_dihedral_angle_3_deg 14.98 r_dihedral_angle_1_deg 5.734 r_scangle_it 5.337 r_scbond_it 3.45 r_mcangle_it 2.058 r_angle_refined_deg 2.007 r_mcbond_it 1.144 r_chiral_restr 0.224 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 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 5240 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing