☰ Navigation Tabs
Crystal structure of a cell-wall invertase (D239A) 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, 0.1 zinc acetate, 20% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.271 α = 90 b = 106.271 β = 90 c = 50.434 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 X13 0.8073 EMBL/DESY, HAMBURG X13
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 2.84 20 99 2.1 14805 13798 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 2.84 2.9 99.4 2.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2AC1 2.84 18.66 13798 730 98.62 0.19653 0.19358 0.253 0.2416 RANDOM 39.242
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.423 r_dihedral_angle_3_deg 18.487 r_dihedral_angle_4_deg 17.359 r_dihedral_angle_1_deg 6.532 r_scangle_it 1.387 r_angle_refined_deg 1.272 r_scbond_it 0.768 r_mcangle_it 0.764 r_mcbond_it 0.411 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.423 r_dihedral_angle_3_deg 18.487 r_dihedral_angle_4_deg 17.359 r_dihedral_angle_1_deg 6.532 r_scangle_it 1.387 r_angle_refined_deg 1.272 r_scbond_it 0.768 r_mcangle_it 0.764 r_mcbond_it 0.411 r_nbtor_refined 0.309 r_symmetry_metal_ion_refined 0.253 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.193 r_symmetry_hbond_refined 0.178 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.092 r_bond_refined_d 0.008 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 4298 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 142
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection DENZO data reduction SCALEPACK data scaling