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Structure of the dTDP-sugar epimerase StrM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 291 10% PEG 6,000, 30% PEG 300, 100
mM CaCl2, 50 mM Tris pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.47 50.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.349 α = 90 b = 132.361 β = 90 c = 77.557 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 2018-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.326 66.18 74 0.996 10 6.3 36601
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 1.326 1.433 20.8 0.304
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 4HMZ 1.326 66.18 36601 1849 71.823 0.201 0.1996 0.1996 0.2344 0.2343 15.358
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] -0.186 0.232 -0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.322 r_dihedral_angle_4_deg 21.655 r_dihedral_angle_3_deg 13.875 r_lrange_it 7.802 r_scangle_it 7.628 r_dihedral_angle_1_deg 5.907 r_scbond_it 5.639 r_mcangle_it 3.638 r_mcbond_it 3.587 r_angle_refined_deg 1.777
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.322 r_dihedral_angle_4_deg 21.655 r_dihedral_angle_3_deg 13.875 r_lrange_it 7.802 r_scangle_it 7.628 r_dihedral_angle_1_deg 5.907 r_scbond_it 5.639 r_mcangle_it 3.638 r_mcbond_it 3.587 r_angle_refined_deg 1.777 r_nbtor_refined 0.315 r_nbd_refined 0.214 r_symmetry_xyhbond_nbd_refined 0.193 r_symmetry_nbd_refined 0.165 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.13 r_gen_planes_refined 0.012 r_bond_refined_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1546 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling STARANISO data scaling MoRDa phasing