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X-ray structure of gene product from arabidopsis thaliana at3g03250, a putative UDP-glucose pyrophosphorylase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 293 1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K 2 5.5 293 1 mg/ml protein, 30% PEG2K, 0.100M MES/ACETATE, 5% DMSO, vapor diffusion, hanging drop, pH 5.5, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.68 α = 90 b = 58.863 β = 100.4 c = 89.862 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 MARMOSAIC 225 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-03-13 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 300 mm CCD HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR 2005-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM 2 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 1,2 1.863 37.365 98 0.066 17.377 7 79505
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) 1.86 1.9 89.5 0.395 3.224 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.86 50 75518 3986 97.7 0.20319 0.201 0.2016 0.249 0.2483 RANDOM 31.48
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] -0.79 -1.22 -0.25 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.434 r_dihedral_angle_4_deg 17.45 r_dihedral_angle_3_deg 16.783 r_angle_other_deg 16.409 r_scangle_it 6.843 r_dihedral_angle_1_deg 6.359 r_scbond_it 4.837 r_mcangle_it 2.948 r_mcbond_it 1.73 r_angle_refined_deg 1.607
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.434 r_dihedral_angle_4_deg 17.45 r_dihedral_angle_3_deg 16.783 r_angle_other_deg 16.409 r_scangle_it 6.843 r_dihedral_angle_1_deg 6.359 r_scbond_it 4.837 r_mcangle_it 2.948 r_mcbond_it 1.73 r_angle_refined_deg 1.607 r_mcbond_other 0.411 r_nbtor_refined 0.312 r_nbtor_other 0.288 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.214 r_symmetry_vdw_refined 0.198 r_nbd_other 0.168 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.11 r_bond_other_d 0.097 r_gen_planes_other 0.033 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7122 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS phasing RESOLVE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing