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Structure of glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma brucei determined from Laue data
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GD1 PDB ENTRY 1GD1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PROTEIN: 5 MICROL OF 6 MG/ML GGAPDH IN 25 MM TRIS HCL PH 7.8, 0.6M AMMONIUM SULPHATE, 2MM NAD, 1MM DITHIOTHREITOL 1MM NA AZIDE, 1 MM EDTA. PRECIPITANT: 5 MICROL OF 52% SATURATED AMMONIUM SULPHATE, 0.2M N,N-BIS-(2-HYDROXYETHYL)-2-AMINOETHANE SULFONIC ACID PH 6.5, 1MM DITHIOTHREITOL, 1MM NA AZIDE, 1MM EDTA, 20MM 3-PHOSPHOGLYCERATE. RESERVOIR: 1 ML
Crystal Properties Matthews coefficient Solvent content 4.27 71.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.52 α = 90 b = 256.27 β = 90 c = 114.91 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 FILM CEA L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.7 0.489-1.905 SRS PX9.7
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 3.2 7.4 57 0.15 7.2 2.3 34991 1 34.93
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1GD1 3.2 7.399 2.37 34991 1798 57.28 0.1533 0.1498 0.1498 0.2182 0.2183 34.75
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] -4.9115 -0.717 -2.7097
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 22.284 f_angle_d 1.492 f_chiral_restr 0.12 f_bond_d 0.009 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16410 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 324
Software Software Software Name Purpose PHENIX refinement DARESBURY data reduction DARESBURY data scaling MERLOT phasing BIOMOL phasing