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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
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 = 69.327 α = 90 b = 104.585 β = 107.35 c = 90.838 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 monochromator 2005-03-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD QUANTUM 315 double crystal monochromator 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 0.980699 SSRL BL9-2 2 SYNCHROTRON SSRL BEAMLINE BL9-2 0.980699 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 2.25 46.37 96.9 0.093 7.4 3.7 54043 54043 -3 49.5
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 2.25 2.37 87.1 0.507 2.2 3.4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1J0X 2.25 46.37 54043 54043 2892 96.94 0.18587 0.18587 0.18282 0.2428 RANDOM 65.472
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] 0.25 0.14 -0.25 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.49 r_dihedral_angle_4_deg 16.043 r_dihedral_angle_3_deg 13.111 r_dihedral_angle_1_deg 5.77 r_scangle_it 2.817 r_scbond_it 1.945 r_mcangle_it 1.753 r_mcbond_it 1.346 r_angle_refined_deg 1.088 r_angle_other_deg 0.715
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.49 r_dihedral_angle_4_deg 16.043 r_dihedral_angle_3_deg 13.111 r_dihedral_angle_1_deg 5.77 r_scangle_it 2.817 r_scbond_it 1.945 r_mcangle_it 1.753 r_mcbond_it 1.346 r_angle_refined_deg 1.088 r_angle_other_deg 0.715 r_mcbond_other 0.269 r_nbd_refined 0.176 r_nbtor_refined 0.169 r_nbd_other 0.165 r_xyhbond_nbd_refined 0.145 r_symmetry_vdw_other 0.137 r_symmetry_hbond_refined 0.101 r_nbtor_other 0.079 r_symmetry_vdw_refined 0.077 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 10204 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 239
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing