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2-keto-3-deoxygluconate aldolase from Sulfolobus acidocaldarius, native structure in p6522 at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NUW PDB entry 2NUW
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 4.25 71.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.509 α = 90 b = 109.509 β = 90 c = 319.559 γ = 120
Symmetry Space Group P 65 2 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 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 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 2.5 36 90.1 0.155 23.77 33.1 36273 -3 50.216
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 2.55 53 0.39 8 19.8 1194
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 2NUW 2.5 36 40218 36261 1878 90.16 0.177 0.175 0.1834 0.216 0.2192 RANDOM 28.345
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] 2.43 1.21 2.43 -3.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.77 r_dihedral_angle_3_deg 10.74 r_scangle_it 9.896 r_dihedral_angle_4_deg 9.534 r_scbond_it 7.784 r_mcangle_it 4.42 r_mcbond_it 3.684 r_dihedral_angle_1_deg 2.951 r_angle_refined_deg 1.34 r_mcbond_other 1.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.77 r_dihedral_angle_3_deg 10.74 r_scangle_it 9.896 r_dihedral_angle_4_deg 9.534 r_scbond_it 7.784 r_mcangle_it 4.42 r_mcbond_it 3.684 r_dihedral_angle_1_deg 2.951 r_angle_refined_deg 1.34 r_mcbond_other 1.155 r_angle_other_deg 0.861 r_symmetry_vdw_other 0.25 r_nbd_refined 0.211 r_nbtor_refined 0.185 r_nbd_other 0.183 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.14 r_xyhbond_nbd_refined 0.105 r_chiral_restr 0.092 r_nbtor_other 0.087 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 94 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