☰ Navigation Tabs
Crystal structure of a cell-wall invertase (D23A) 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 0.1M sodium cacodylate, 0.1M zinc acetate, 22.5% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.877 α = 90 b = 105.877 β = 90 c = 50.479 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 2006-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 1.0332 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 2.8 30 99.4 3.4 15532 12825 2 1.41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85 100 3.3
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 pdb entry 2AC1 2.8 28.57 12825 776 99.4 0.19153 0.18831 0.191 0.25231 0.2507 RANDOM 45.498
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.206 r_dihedral_angle_3_deg 17.367 r_dihedral_angle_4_deg 14.211 r_dihedral_angle_1_deg 6.065 r_scangle_it 1.533 r_angle_refined_deg 1.333 r_scbond_it 0.905 r_mcangle_it 0.894 r_mcbond_it 0.495 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.206 r_dihedral_angle_3_deg 17.367 r_dihedral_angle_4_deg 14.211 r_dihedral_angle_1_deg 6.065 r_scangle_it 1.533 r_angle_refined_deg 1.333 r_scbond_it 0.905 r_mcangle_it 0.894 r_mcbond_it 0.495 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.085 r_symmetry_metal_ion_refined 0.02 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4287 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 141
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection