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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 4.1 301 0.4M Potassium sodium tartrate tetrahydrate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 301K
Crystal Properties Matthews coefficient Solvent content 2.83 56.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.922 α = 90 b = 72.685 β = 91.07 c = 161.312 γ = 90
Symmetry Space Group C 1 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 RIGAKU JUPITER 210 2005-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.97937 SPring-8 BL45PX
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 1.67 35.6 86.3 0.079 11.39 2.7 145847 145847
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 1.67 1.73 65.9 0.303 3.52 2.2 11116
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 1.67 35.58 131262 131262 14564 100 0.185 0.185 0.182 0.214 RANDOM 19.695
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] 0.19 0.01 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.045 r_dihedral_angle_4_deg 16.533 r_dihedral_angle_3_deg 14.59 r_dihedral_angle_1_deg 5.352 r_scangle_it 4.549 r_scbond_it 2.695 r_mcangle_it 1.679 r_angle_refined_deg 1.533 r_mcbond_it 1.034 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.045 r_dihedral_angle_4_deg 16.533 r_dihedral_angle_3_deg 14.59 r_dihedral_angle_1_deg 5.352 r_scangle_it 4.549 r_scbond_it 2.695 r_mcangle_it 1.679 r_angle_refined_deg 1.533 r_mcbond_it 1.034 r_nbtor_refined 0.318 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.212 r_symmetry_vdw_refined 0.203 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 8808 Nucleic Acid Atoms Solvent Atoms 1023 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Rapid data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing