☰ Navigation Tabs
Crystal structure of 3-deoxy-d-manno-octulosonate 8-phosphate synthase (KDO8PS) from Neisseria meningitidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D9E PDB ENTRY 1D9E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 295 CRYSTALLISATION CONDITIONS: 18.6 MG/ML PROTEIN MIXED 1:1 WITH RESERVOIR LIQUOR CONTAINING 100 MM SODIUM ACETATE PH 4.60, 200 MICROMOLAR PEP, 0.6, 1.6 MOLAR SODIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.515 α = 90 b = 85.295 β = 90 c = 162.686 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 IMAGE PLATE RIGAKU RAXIS IV OSMIC BLUE MIRRORS 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
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 1.75 40 97 0.043 13.4 3.95 111333 31.7
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 1.75 1.81 78.2 0.368 2.7 4.16
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 1D9E 1.75 40 111333 105744 5588 97 0.197 0.196 0.2034 0.235 0.2423 RANDOM 30.27
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] 0.91 0.2 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.994 r_dihedral_angle_4_deg 17.825 r_dihedral_angle_3_deg 13.796 r_dihedral_angle_1_deg 5.619 r_mcangle_it 2.874 r_mcbond_it 1.869 r_scangle_it 1.683 r_angle_refined_deg 1.306 r_scbond_it 1.041 r_angle_other_deg 0.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.994 r_dihedral_angle_4_deg 17.825 r_dihedral_angle_3_deg 13.796 r_dihedral_angle_1_deg 5.619 r_mcangle_it 2.874 r_mcbond_it 1.869 r_scangle_it 1.683 r_angle_refined_deg 1.306 r_scbond_it 1.041 r_angle_other_deg 0.817 r_mcbond_other 0.665 r_symmetry_vdw_refined 0.242 r_nbd_other 0.222 r_symmetry_vdw_other 0.215 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.17 r_metal_ion_refined 0.143 r_nbtor_other 0.112 r_chiral_restr 0.073 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7748 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 30
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction d*TREK data reduction MOLREP phasing