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2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure at 1.8 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W3N PDB ENTRY 1w3n
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 4.45 72.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.16 α = 90 b = 108.16 β = 90 c = 171.852 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 2004-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 1.8 30 99.9 0.096 14.14 10.9 107995 -3 30.218
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 1.8 1.88 99.8 0.559 2.3 4 13009
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 (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 PDB ENTRY 1w3n 1.8 29.35 108033 107995 5421 99.96 0.158 0.157 0.1707 0.179 0.1914 RANDOM 13.196
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] 2.18 1.09 2.18 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.432 r_dihedral_angle_4_deg 12.683 r_scangle_it 11.714 r_dihedral_angle_3_deg 11.35 r_scbond_it 8.597 r_mcangle_it 4.454 r_mcbond_it 4.23 r_dihedral_angle_1_deg 3.898 r_angle_refined_deg 1.472 r_mcbond_other 1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.432 r_dihedral_angle_4_deg 12.683 r_scangle_it 11.714 r_dihedral_angle_3_deg 11.35 r_scbond_it 8.597 r_mcangle_it 4.454 r_mcbond_it 4.23 r_dihedral_angle_1_deg 3.898 r_angle_refined_deg 1.472 r_mcbond_other 1.28 r_angle_other_deg 0.891 r_nbd_refined 0.211 r_nbd_other 0.186 r_nbtor_refined 0.185 r_symmetry_vdw_other 0.174 r_xyhbond_nbd_refined 0.144 r_symmetry_hbond_refined 0.143 r_symmetry_vdw_refined 0.103 r_chiral_restr 0.101 r_nbtor_other 0.09 r_metal_ion_refined 0.025 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 410 Heterogen Atoms 1
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ProDC data collection XDS data reduction