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Crystal Structure of a Putative UDP-glucose Pyrophosphorylase from Arabidopsis Thaliana with Bound UTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 vapor diffusion, hanging drop with micro-seeding 273 Protein solution (10 mg/ml protein,
0.050 M sodium chloride, 0.0003 M TCEP, 0.005 M Tris PH 8.0) mixed
in a 1:1 ratio with Well solution (
28 % PEG 2K, 5% DMSO, 0.10 M MES/Acetate pH 5.5), crystals soaked in well solution
supplemented with 0.002 M UTP, vapor diffusion, hanging drop with micro-seeding, temperature 273K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.683 α = 90 b = 59.679 β = 100.38 c = 89.813 γ = 90
Symmetry Space Group C 1 2 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 CCD BRUKER PROTEUM-R MONTEL OPTICS 2006-05-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.85 70.481 99.4 0.0353 23.9 14.3 83235
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.9 100 0.3115 3.19 5.09 6377
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1Z90 1.85 70.481 83222 4158 99.371 0.195 0.192 0.2192 0.239 0.2541 RANDOM 11.405
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] -0.363 -0.235 -0.398 0.676
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.005 r_dihedral_angle_3_deg 14.536 r_dihedral_angle_4_deg 13.597 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.454 r_scbond_it 2.253 r_angle_refined_deg 1.902 r_mcangle_it 1.298 r_mcbond_it 0.868 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.005 r_dihedral_angle_3_deg 14.536 r_dihedral_angle_4_deg 13.597 r_dihedral_angle_1_deg 5.963 r_scangle_it 3.454 r_scbond_it 2.253 r_angle_refined_deg 1.902 r_mcangle_it 1.298 r_mcbond_it 0.868 r_nbtor_refined 0.308 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7132 Nucleic Acid Atoms Solvent Atoms 871 Heterogen Atoms 62
Software Software Software Name Purpose SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction SADABS data scaling