☰ Navigation Tabs
Crystal structure of alkaline/neutral invertase InvB from Anabaena sp. PCC 7120 complexed with sucrose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Z73
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 289 0.7M lithium chloride, 6% polyethylene glycol 6000, 0.1M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.77 55.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.946 α = 90 b = 82.171 β = 119.13 c = 97.446 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 ADSC QUANTUM 315r 2016-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97916 SSRF BL17U1
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 1.95 50 95.7 0.096 13.1 3.5 80206
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 1.95 2.02 98.1 0.537 2.4 3.5
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 5Z73 1.95 31.35 76001 4009 95.35 0.20978 0.20828 0.23854 0.2534 RANDOM 37.03
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] -1.1 0.19 -0.39 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.401 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 4.872 r_long_range_B_refined 4.076 r_long_range_B_other 4.073 r_scangle_other 2.638 r_mcangle_it 2.33 r_mcangle_other 2.329 r_scbond_it 1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.401 r_dihedral_angle_4_deg 16.148 r_dihedral_angle_3_deg 12.433 r_dihedral_angle_1_deg 4.872 r_long_range_B_refined 4.076 r_long_range_B_other 4.073 r_scangle_other 2.638 r_mcangle_it 2.33 r_mcangle_other 2.329 r_scbond_it 1.511 r_scbond_other 1.511 r_mcbond_it 1.36 r_mcbond_other 1.36 r_angle_refined_deg 1.114 r_angle_other_deg 0.735 r_chiral_restr 0.062 r_bond_refined_d 0.005 r_bond_other_d 0.005 r_gen_planes_refined 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7008 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection