☰ Navigation Tabs
Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MXS PDB ENTRY 1MXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 301 0.2M Calcium Chloride dihydrate, 0.1M Sodium Acetate trihydrate, 20% v/v iso-Propanol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal Properties Matthews coefficient Solvent content 2.37 48.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.686 α = 90 b = 66.686 β = 90 c = 241.301 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 100 IMAGE PLATE RIGAKU RAXIS V mirrors 2005-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-D 1.5418
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 2.53 30.8 99.9 0.055 33.47 10.1 7273 7273
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 2.53 2.62 100 0.298 8.55 10.2 697
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1MXS 2.53 30.8 6558 6558 712 100 0.171 0.171 0.164 0.241 RANDOM 24.301
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] 0.57 0.28 0.57 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_3_deg 21.226 r_dihedral_angle_4_deg 18.869 r_scangle_it 7.347 r_dihedral_angle_1_deg 7.018 r_scbond_it 4.478 r_mcangle_it 2.751 r_angle_refined_deg 2.58 r_mcbond_it 1.807 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.292 r_dihedral_angle_3_deg 21.226 r_dihedral_angle_4_deg 18.869 r_scangle_it 7.347 r_dihedral_angle_1_deg 7.018 r_scbond_it 4.478 r_mcangle_it 2.751 r_angle_refined_deg 2.58 r_mcbond_it 1.807 r_nbtor_refined 0.327 r_symmetry_hbond_refined 0.278 r_nbd_refined 0.26 r_symmetry_vdw_refined 0.255 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.163 r_bond_refined_d 0.033 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1483 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing