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Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070 in complex with UDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other apo-TaGalU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 292.15 sodium citrate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.75 55.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.752 α = 90 b = 65.752 β = 90 c = 329.552 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M 2017-05-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976300 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 82.53 100 0.09 0.093 0.024 1 29.1 26.4 43788
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 1.26 1.28 0.24 1 3.86 26.9
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 apo-TaGalU 2.1 82.524 43675 2094 99.918 0.177 0.1748 0.1738 0.2209 0.2192 43.301
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] 1.638 1.638 -3.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.89 r_dihedral_angle_3_deg 14.255 r_lrange_it 8.532 r_lrange_other 8.508 r_dihedral_angle_2_deg 8.227 r_dihedral_angle_1_deg 6.951 r_scangle_it 6.157 r_scangle_other 6.156 r_scbond_it 4.133 r_scbond_other 4.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.89 r_dihedral_angle_3_deg 14.255 r_lrange_it 8.532 r_lrange_other 8.508 r_dihedral_angle_2_deg 8.227 r_dihedral_angle_1_deg 6.951 r_scangle_it 6.157 r_scangle_other 6.156 r_scbond_it 4.133 r_scbond_other 4.132 r_mcangle_it 4.127 r_mcangle_other 4.127 r_mcbond_it 2.963 r_mcbond_other 2.954 r_angle_refined_deg 1.855 r_angle_other_deg 0.576 r_nbd_refined 0.221 r_symmetry_nbd_other 0.196 r_nbd_other 0.188 r_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.172 r_symmetry_nbd_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_other 0.11 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.08 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4404 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling XDS data reduction Aimless data scaling MOLREP phasing