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Crystal structure of UDP-glucose pyrophosphorylase from Thermocrispum agreste DSM 44070
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JUJ 3JUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 292.15 Bis-Tris-Propane, PEG3350, KSCN, Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.63 53.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.086 α = 90 b = 78.593 β = 93.885 c = 89.788 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) 0.976 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.75 89.58 99.8 0.059 0.069 0.035 0.99 10.5 3.7 67139
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 1.75 1.78 99.7 0.866 1.025 0.541 0.651 1.3 3.5
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 3JUJ 1.75 48.022 67108 3270 99.761 0.198 0.196 0.1961 0.2262 0.2261 32.816
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] 2.122 -1.419 -0.948 -0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 18.407 r_dihedral_angle_6_deg 16.866 r_dihedral_angle_3_deg 14.084 r_dihedral_angle_2_deg 10.216 r_lrange_it 7.073 r_lrange_other 6.959 r_dihedral_angle_1_deg 6.756 r_scangle_it 4.341 r_scangle_other 4.34 r_mcangle_it 3.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 18.407 r_dihedral_angle_6_deg 16.866 r_dihedral_angle_3_deg 14.084 r_dihedral_angle_2_deg 10.216 r_lrange_it 7.073 r_lrange_other 6.959 r_dihedral_angle_1_deg 6.756 r_scangle_it 4.341 r_scangle_other 4.34 r_mcangle_it 3.06 r_mcangle_other 3.06 r_scbond_it 2.919 r_scbond_other 2.919 r_mcbond_it 2.113 r_mcbond_other 2.113 r_angle_refined_deg 1.649 r_angle_other_deg 0.639 r_metal_ion_refined 0.304 r_nbd_refined 0.208 r_nbd_other 0.176 r_symmetry_nbd_other 0.168 r_nbtor_refined 0.155 r_xyhbond_nbd_refined 0.154 r_symmetry_nbd_refined 0.11 r_symmetry_xyhbond_nbd_refined 0.106 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.072 r_chiral_restr_other 0.049 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4384 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing