☰ Navigation Tabs
Structure analysis of the type II cohesin dyad from the adaptor ScaA scaffoldin of Acetivibrio cellulolyticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZV9 PDB ENTRY 1ZV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 0.15M citric acid pH 3.5, 16% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 49.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.225 α = 100.25 b = 73.912 β = 94.26 c = 90.793 γ = 112.15
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 315 2007-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.930 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.57 30 97 0.077 0.077 23.9 3.8 192139 17.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.57 1.6 95.4 0.446 0.446 2.1 3.7 8616
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 1ZV9 1.57 29.63 176887 9366 97 0.1805 0.17813 0.1896 0.22554 0.2353 RANDOM 15.626
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] -1.11 -0.36 0.49 0.75 0.21 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.396 r_dihedral_angle_4_deg 15.841 r_dihedral_angle_3_deg 11.116 r_scangle_it 7.76 r_dihedral_angle_1_deg 7.2 r_scbond_it 5.726 r_mcangle_it 3.585 r_mcbond_it 2.354 r_rigid_bond_restr 1.917 r_angle_refined_deg 1.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.396 r_dihedral_angle_4_deg 15.841 r_dihedral_angle_3_deg 11.116 r_scangle_it 7.76 r_dihedral_angle_1_deg 7.2 r_scbond_it 5.726 r_mcangle_it 3.585 r_mcbond_it 2.354 r_rigid_bond_restr 1.917 r_angle_refined_deg 1.333 r_angle_other_deg 0.845 r_mcbond_other 0.728 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10245 Nucleic Acid Atoms Solvent Atoms 2156 Heterogen Atoms 126
Software Software Software Name Purpose ProDC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling