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Crystal Structure of 2-keto-3-deoxyoctulosonate 8-phosphate phosphohydrolase from Haemophilus influenzae in complex with transition state mimic
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K1E PDB entry 1k1e
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 290 100 mM Tris, 30% polyethylene glycol 3350. Crystal soaked with 20 mM NaVN4, 20 mM KDO for 3 days. Crystal dragged through Paratone prior to flash cooling, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.846 α = 90 b = 79.846 β = 90 c = 52.151 γ = 90
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 Bruker Platinum 135 Helios multi-layer optics 2010-01-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 1.8 29.5 95.6 0.0573 13.68 7.9 14655 2 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 1.8 1.89 91.4 0.3813 2.4 5.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1k1e 1.8 29.463 1.38 14655 775 95.65 0.1502 0.1467 0.1455 0.1732 0.1778 17.75
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.838 f_angle_d 1.136 f_chiral_restr 0.067 f_bond_d 0.014 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1352 Nucleic Acid Atoms Solvent Atoms 177 Heterogen Atoms 21
Software Software Software Name Purpose PROTEUM PLUS data collection MOLREP phasing PHENIX refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling