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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 6000, 30% PEG 300, 100
mM CaCl2, 50 mM Tris pH 7.0
+ 10 mM dTDP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.376 α = 90 b = 131.542 β = 90 c = 78.539 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 2019-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 Diamond I04-1
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 1.9 50.42 99.4 0.991 5.5 4.3 17624
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 1.9 1.94 0.312
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 1.9 50.42 17601 925 99.138 0.203 0.2009 0.2008 0.2495 0.2496 28.068
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] -1.435 0.191 1.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.323 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 15.799 r_lrange_it 8.382 r_dihedral_angle_1_deg 6.567 r_scangle_it 4.45 r_mcangle_it 3.636 r_scbond_it 2.878 r_mcbond_it 2.272 r_angle_refined_deg 1.401
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.323 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 15.799 r_lrange_it 8.382 r_dihedral_angle_1_deg 6.567 r_scangle_it 4.45 r_mcangle_it 3.636 r_scbond_it 2.878 r_mcbond_it 2.272 r_angle_refined_deg 1.401 r_nbtor_refined 0.312 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.15 r_chiral_restr 0.107 r_gen_planes_refined 0.007 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1567 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MoRDa phasing Coot model building