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Crystal structure of a glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GAD PDB ENTRY 1GAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 TrcrA.00814.b.B1.PS01922 at 29.1 mg/mL against JCSG+ screen condition G8 (0.15 M DL-malic acid, 25% PEG3350), cryoprotectant: 15% ethylene glycol, crystal tracking ID 246268g8, unique puck ID roi5-9, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.53 51.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.49 α = 90 b = 80.49 β = 90 c = 203.06 γ = 120
Symmetry Space Group P 32 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 RAYONIX MX-300 2012-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.65 50 99.9 0.092 16.1 10.3 92667 92582 -3 25.482
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 1.65 1.69 100 0.434 5.06
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 1GAD 1.65 48.61 92504 4627 99.92 0.1337 0.1317 0.1475 0.1702 0.1751 RANDOM 22.6967
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] 0.14 0.14 0.14 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_sphericity_free 29.029 r_dihedral_angle_4_deg 16.339 r_dihedral_angle_3_deg 12.165 r_sphericity_bonded 7.039 r_dihedral_angle_1_deg 6.341 r_rigid_bond_restr 2.23 r_mcangle_it 1.766 r_angle_refined_deg 1.396 r_mcbond_other 1.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_sphericity_free 29.029 r_dihedral_angle_4_deg 16.339 r_dihedral_angle_3_deg 12.165 r_sphericity_bonded 7.039 r_dihedral_angle_1_deg 6.341 r_rigid_bond_restr 2.23 r_mcangle_it 1.766 r_angle_refined_deg 1.396 r_mcbond_other 1.357 r_mcbond_it 1.356 r_angle_other_deg 0.778 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4934 Nucleic Acid Atoms Solvent Atoms 645 Heterogen Atoms 112
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction