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Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070 in complex with UDP-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Other TgalU-nat
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292.15 Bis-Tris-Propan, polyethylene glycol 3350, potassium thiocyanate (KSCN) and ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.65 53.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.036 α = 90 b = 78.433 β = 93.904 c = 90.289 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2019-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976300 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 90.08 99.8 0.049 0.02 0.99 12.7 6.7 87903
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 99.8 1.25 0.51 0.71 6.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE TgalU-nat 1.6 90.079 87901 4258 99.819 0.178 0.1762 0.2037 0.2059 30.66
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] 1.359 -1.1 -0.313 -0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 24.433 r_dihedral_angle_6_deg 16.909 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_2_deg 8.777 r_lrange_it 7.075 r_lrange_other 7.074 r_dihedral_angle_1_deg 6.531 r_scangle_it 4.723 r_scangle_other 4.723 r_scbond_it 3.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 24.433 r_dihedral_angle_6_deg 16.909 r_dihedral_angle_3_deg 13.664 r_dihedral_angle_2_deg 8.777 r_lrange_it 7.075 r_lrange_other 7.074 r_dihedral_angle_1_deg 6.531 r_scangle_it 4.723 r_scangle_other 4.723 r_scbond_it 3.247 r_scbond_other 3.246 r_mcangle_it 3.05 r_mcangle_other 3.05 r_mcbond_it 2.146 r_mcbond_other 2.116 r_angle_refined_deg 1.79 r_angle_other_deg 0.671 r_nbd_refined 0.207 r_nbd_other 0.174 r_symmetry_nbd_other 0.164 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.149 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.126 r_chiral_restr_other 0.1 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4371 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing