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Crystal Structure of 3-Phosphopglycerate Kinase of Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LTK PDB ENTRY 1LTK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.25 298 Ammonium Sulfate, Hepes Buffer, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.58 65.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.386 α = 90 b = 131.386 β = 90 c = 262.617 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARRESEARCH 2001-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.9790 APS 17-ID
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 50 94.8 0.069 15.7 35575
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 71.6 0.297
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 1LTK 2.7 19.9 33703 1769 94.7 0.23276 0.23061 0.2257 0.27367 0.2651 RANDOM 47.584
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] -0.07 -0.03 -0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.857 r_dihedral_angle_3_deg 18.553 r_dihedral_angle_4_deg 11.834 r_dihedral_angle_1_deg 5.176 r_scangle_it 1.652 r_angle_refined_deg 1.13 r_scbond_it 0.908 r_mcangle_it 0.657 r_mcbond_it 0.339 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.857 r_dihedral_angle_3_deg 18.553 r_dihedral_angle_4_deg 11.834 r_dihedral_angle_1_deg 5.176 r_scangle_it 1.652 r_angle_refined_deg 1.13 r_scbond_it 0.908 r_mcangle_it 0.657 r_mcbond_it 0.339 r_chiral_restr 0.071 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6370 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 20
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction MOLREP phasing