☰ Navigation Tabs
Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EUA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.5 277 22.5% PEG-1000, 0.1M Tris pH 7.5 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.543 α = 90 b = 113.194 β = 90 c = 128.397 γ = 90
Symmetry Space Group C 2 2 21
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 2003-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 2.3 34.14 97.1 0.09 11.2 3.1 25311 50.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 82.2 0.681 1.6 2 1556
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 1eua 2.3 34.14 24015 1286 96.8 0.17887 0.17663 0.1861 0.22106 0.2267 RANDOM 40.26
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] -0.23 0.22 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_4_deg 22.552 r_dihedral_angle_3_deg 17.731 r_scangle_it 6.578 r_dihedral_angle_1_deg 6.489 r_scbond_it 4.738 r_mcangle_it 2.812 r_mcbond_it 1.893 r_angle_refined_deg 1.584 r_angle_other_deg 0.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.619 r_dihedral_angle_4_deg 22.552 r_dihedral_angle_3_deg 17.731 r_scangle_it 6.578 r_dihedral_angle_1_deg 6.489 r_scbond_it 4.738 r_mcangle_it 2.812 r_mcbond_it 1.893 r_angle_refined_deg 1.584 r_angle_other_deg 0.846 r_mcbond_other 0.542 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.201 r_symmetry_vdw_other 0.197 r_xyhbond_nbd_refined 0.187 r_nbd_other 0.177 r_nbtor_refined 0.174 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_other 0.138 r_nbtor_other 0.092 r_chiral_restr 0.084 r_bond_refined_d 0.016 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 4650 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling