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3.0 A RESOLUTION CRYSTAL STRUCTURE OF GLYCOSOMAL PYRUVATE PHOSPHATE DIKINASE FROM TRYPANOSOMA BRUCEI
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DIK PDB ENTRY 1DIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 HANGING DROP, 2 MICROLITER PROTEIN AND 2 MICROLITER PRECIPITANT SOLUTION. PROTEIN SOLUTION. 50 MG/ML, 20 MM IMIDAZOLE PH 7.0, 100 MM NACL, 100 MM MGCL2, 20% (V/V) GLYCEROL. PRECIPITANT SOLUTION. 0.1 M BICINE PH 8.8, 1.5 % (W/V) PEG 5000 MONOMETHYLETHER, 10 % (V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.1 58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.17 α = 90 b = 153.5 β = 90 c = 65.46 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 277 IMAGE PLATE MARRESEARCH 2000-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 LURE DW32
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 24 96 0.09 14.8 5.3 24120 61
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 3 3.1 88.6 0.28 3.1 3.4
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 1DIK 2.997 23.938 1.62 24115 1163 95.73 0.1687 0.1649 0.1673 0.2415 0.2398 81.08
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] 6.1816 -1.6729 -4.8838
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.423 f_angle_d 1.345 f_chiral_restr 0.082 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6935 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction BIOMOL data scaling CNS phasing