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Structure of the 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) from Coxiella burnetii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K8D PDB entry 3K8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 0.17 M ammonium acetate, 0.085 M Na citrate, 25.5% PEG 4000, 15% glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.2 44.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.752 α = 90 b = 51.616 β = 111.92 c = 78.874 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 SATURN 944 2011-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.8 100 97.9 0.053 39.4 9.9 23582 23093 -3
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 1.83 88 0.454 2.3 3.6 1186
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 3K8D 1.8 25.62 23663 22946 1184 96.97 0.19026 0.1882 0.2062 0.22746 0.2422 RANDOM 39.645
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 0.27 2.06 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 15.824 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 6.181 r_scangle_it 4.418 r_scbond_it 2.781 r_mcangle_it 1.747 r_angle_refined_deg 1.653 r_mcbond_it 1.018 r_angle_other_deg 0.976
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.052 r_dihedral_angle_4_deg 15.824 r_dihedral_angle_3_deg 14.428 r_dihedral_angle_1_deg 6.181 r_scangle_it 4.418 r_scbond_it 2.781 r_mcangle_it 1.747 r_angle_refined_deg 1.653 r_mcbond_it 1.018 r_angle_other_deg 0.976 r_mcbond_other 0.301 r_chiral_restr 0.101 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 1921 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 5
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling