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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom resolution reveals intriguing extra electron density in the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J0X pdb entry 1J0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 30% PEG 3350; 200 MILLIMOLAR NA F; 100 MILLIMOLAR BIS-TRIS-PROPANE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.687 α = 90 b = 106.056 β = 107.24 c = 91.057 γ = 90
Symmetry Space Group P 1 21 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 QUANTUM 315 double crystal 2005-03-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD QUANTUM 315 double crystal 2005-03-04 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9807 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9807 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 46.625 98 0.101 7.9 3.5 42843 42843 -3 68.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 2.5 2.64 97.8 0.484 2.2 3.6 6197
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1J0X 2.5 43.48 40675 40675 2147 97.69 0.17575 0.17575 0.17352 0.1857 0.21677 0.1858 RANDOM 48.808
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] 4.22 1.59 -1.07 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.973 r_dihedral_angle_4_deg 16.91 r_dihedral_angle_3_deg 13.659 r_dihedral_angle_1_deg 5.693 r_scangle_it 2.797 r_scbond_it 1.924 r_mcangle_it 1.647 r_mcbond_it 1.257 r_angle_refined_deg 1.08 r_angle_other_deg 0.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.973 r_dihedral_angle_4_deg 16.91 r_dihedral_angle_3_deg 13.659 r_dihedral_angle_1_deg 5.693 r_scangle_it 2.797 r_scbond_it 1.924 r_mcangle_it 1.647 r_mcbond_it 1.257 r_angle_refined_deg 1.08 r_angle_other_deg 0.712 r_symmetry_hbond_refined 0.283 r_mcbond_other 0.249 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.187 r_symmetry_vdw_other 0.184 r_nbtor_refined 0.173 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.15 r_nbtor_other 0.08 r_chiral_restr 0.059 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10184 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 215
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing