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2.6 Angstrom Crystal Structure of Putative Phosphoglycerate Mutase 1 from Toxoplasma gondii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein - 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3, Screen - Classics II (G12), 0.2M Magnesium chloride, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.05 39.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.182 α = 90 b = 149.474 β = 90 c = 72.12 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 100 CCD MARMOSAIC 225 mm CCD Beryllium lenses 2013-11-18 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) 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 2.6 30 100 0.106 0.106 18.3 7.3 33033 33033 -3 52
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.645 0.645 3.3 7.4 1604
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1XQ9 2.6 29.72 31317 31317 1671 99.77 0.19925 0.19925 0.19717 0.23881 0.233 RANDOM 56.296
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] -1.48 2.24 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.112 r_dihedral_angle_3_deg 11.868 r_dihedral_angle_4_deg 11.554 r_long_range_B_refined 6.815 r_long_range_B_other 6.815 r_scangle_other 4.75 r_mcangle_other 3.542 r_mcangle_it 3.541 r_scbond_it 3.003 r_scbond_other 3.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.112 r_dihedral_angle_3_deg 11.868 r_dihedral_angle_4_deg 11.554 r_long_range_B_refined 6.815 r_long_range_B_other 6.815 r_scangle_other 4.75 r_mcangle_other 3.542 r_mcangle_it 3.541 r_scbond_it 3.003 r_scbond_other 3.003 r_dihedral_angle_1_deg 2.382 r_mcbond_it 2.268 r_mcbond_other 2.255 r_angle_refined_deg 1.626 r_angle_other_deg 1.217 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7719 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 4
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling