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dTDP-sugar epimerase from Coxiella burnetii in complex with dTDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 7% PEG 4000 (w/v),
30% PEG 400, 5% dTDP (v/v),
29 mM citrate buffer
pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.882 α = 90 b = 82.151 β = 90 c = 163.831 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2018-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.87 81.915 84.8 0.998 12.5 6.6 37452
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.995 25 0.67
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2IXI 1.87 81.915 37452 1856 84.439 0.21 0.209 0.2142 0.2366 0.2416 40.645
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] 0.05 0.008 -0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.034 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 16.799 r_lrange_it 8.622 r_lrange_other 8.62 r_dihedral_angle_1_deg 7.615 r_scangle_it 6.383 r_scangle_other 6.382 r_mcangle_it 4.729 r_mcangle_other 4.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.034 r_dihedral_angle_4_deg 18.259 r_dihedral_angle_3_deg 16.799 r_lrange_it 8.622 r_lrange_other 8.62 r_dihedral_angle_1_deg 7.615 r_scangle_it 6.383 r_scangle_other 6.382 r_mcangle_it 4.729 r_mcangle_other 4.696 r_scbond_it 4.2 r_scbond_other 4.199 r_mcbond_it 3.535 r_mcbond_other 3.498 r_angle_refined_deg 1.588 r_angle_other_deg 1.287 r_nbd_other 0.288 r_symmetry_nbd_refined 0.265 r_symmetry_xyhbond_nbd_refined 0.218 r_nbd_refined 0.203 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_other 0.111 r_ncsr_local_group_1 0.097 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.083 r_xyhbond_nbd_other 0.051 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3120 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 154
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling autoPROC data scaling autoPROC data processing Coot model building STARANISO data scaling MoRDa phasing