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2.05 Angstrom Crystal Structure of Ribulose-phosphate 3-epimerase from Toxoplasma gondii.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 295 Protein: 7.4 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3;
Screen: Classics II (A1), 2M Ammonium sulfate, 0.1M Citric acid pH 3.5. , VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.05 59.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.51 α = 90 b = 138.51 β = 90 c = 349.329 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD Beryllium lenses 2012-11-18 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 2.05 30 100 0.072 0.072 20.1 4.5 81012 81012 -3 32.6
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 2.05 2.09 100 0.615 0.615 2.4 4.5 3999
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3QC3 2.05 29.88 76865 76865 4056 99.88 0.15126 0.15126 0.14941 0.161 0.18685 0.192 RANDOM 39.93
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] 0.12 0.06 0.12 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.956 r_dihedral_angle_4_deg 19.199 r_dihedral_angle_3_deg 11.142 r_long_range_B_refined 7.956 r_long_range_B_other 7.737 r_scangle_other 4.703 r_scbond_it 3.164 r_dihedral_angle_1_deg 3.112 r_scbond_other 2.997 r_mcangle_other 2.732
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.956 r_dihedral_angle_4_deg 19.199 r_dihedral_angle_3_deg 11.142 r_long_range_B_refined 7.956 r_long_range_B_other 7.737 r_scangle_other 4.703 r_scbond_it 3.164 r_dihedral_angle_1_deg 3.112 r_scbond_other 2.997 r_mcangle_other 2.732 r_mcangle_it 2.73 r_mcbond_it 1.834 r_mcbond_other 1.833 r_angle_refined_deg 1.434 r_angle_other_deg 0.719 r_chiral_restr 0.087 r_gen_planes_refined 0.019 r_gen_planes_other 0.017 r_bond_refined_d 0.01 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6761 Nucleic Acid Atoms Solvent Atoms 513 Heterogen Atoms 69
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling