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Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Toxoplasma gondii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CPS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 TOGOA.00914.A.A1.PW28008 23.8 MG/ ML, PH 5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PACT F11, 0.2 M Sodium citrate, 0.1M Bis Tris propand pH 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.367 α = 90 b = 104.322 β = 90 c = 146.625 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2010-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 2.25 50 99.7 0.12 5.7 5.6 75704
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 2.25 2.29 98.7 0.481 5.7
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 3CPS 2.25 50 75385 3830 0.175 0.172 0.1829 0.216 0.2246 RANDOM 23.444
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] -1.01 -0.24 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.585 r_dihedral_angle_4_deg 21.602 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_1_deg 6.212 r_scangle_it 2.431 r_scbond_it 1.541 r_angle_refined_deg 1.277 r_mcangle_it 0.88 r_angle_other_deg 0.866 r_mcbond_it 0.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.585 r_dihedral_angle_4_deg 21.602 r_dihedral_angle_3_deg 13.665 r_dihedral_angle_1_deg 6.212 r_scangle_it 2.431 r_scbond_it 1.541 r_angle_refined_deg 1.277 r_mcangle_it 0.88 r_angle_other_deg 0.866 r_mcbond_it 0.459 r_mcbond_other 0.106 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10169 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 232
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling