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2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius in complex with pyruvate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other native structure of KDGA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 30% PEG400, 0.1M HEPES, 0.2M Magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.47 72.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.09 α = 90 b = 109.09 β = 90 c = 171.29 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 4 2005-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 99.6 0.056 17.6 6.2 41289 -3 52.971
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 2.5 2.65 97.1 0.348 5.3 4.2 6379
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 native structure of KDGA 2.5 47.25 41249 2131 99.6 0.16 0.159 0.1665 0.191 0.2026 RANDOM 29.73
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] 3.58 1.79 3.58 -5.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.905 r_dihedral_angle_3_deg 10.846 r_dihedral_angle_4_deg 10.748 r_scangle_it 10.47 r_scbond_it 8.145 r_mcangle_it 4.228 r_mcbond_it 3.651 r_dihedral_angle_1_deg 3.059 r_angle_refined_deg 1.327 r_mcbond_other 1.138
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.905 r_dihedral_angle_3_deg 10.846 r_dihedral_angle_4_deg 10.748 r_scangle_it 10.47 r_scbond_it 8.145 r_mcangle_it 4.228 r_mcbond_it 3.651 r_dihedral_angle_1_deg 3.059 r_angle_refined_deg 1.327 r_mcbond_other 1.138 r_angle_other_deg 0.846 r_nbd_refined 0.212 r_symmetry_vdw_other 0.197 r_nbtor_refined 0.184 r_nbd_other 0.179 r_symmetry_vdw_refined 0.154 r_symmetry_hbond_refined 0.131 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.091 r_nbtor_other 0.087 r_symmetry_metal_ion_refined 0.07 r_metal_ion_refined 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4598 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ProDC data collection XDS data reduction XSCALE data scaling