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Crystal structure of a cell-wall invertase (E203Q) from Arabidopsis thaliana in complex with sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AC1 PDB ENTRY 2AC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 25% PEG 4000, 0.1M zinc acetate, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.454 α = 90 b = 106.454 β = 90 c = 50.548 γ = 120
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 MAR CCD 165 mm 2005-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 30 99.7 19700 18370 2 1.41 50.9
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 2.6 2.64 98 0.462 2.29
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 2AC1 2.6 19.51 18024 18024 951 91.5 0.205 0.205 0.2148 0.268 0.2793 RANDOM 33.4
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.4 c_scangle_it 2.4 c_mcangle_it 2.14 c_scbond_it 1.6 c_angle_deg 1.5 c_mcbond_it 1.26 c_improper_angle_d 0.94 c_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4315 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 65
Software Software Software Name Purpose CNS refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling CNS phasing