☰ Navigation Tabs
Scabin toxin from Streptomyces scabies in complex with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAZ PDB entry 5DAZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 294 100 mM potassium chloride, 50 mM sodium cacodylate trihydrate, pH 6.0, 16% PEG1000, 0.5 mM spermine
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.04 α = 90 b = 62.26 β = 100.3 c = 38.08 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 RAYONIX MX-300 2016-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.7 42.34 99.7 0.052 0.06 0.031 0.999 15.4 3.8 21771 25.14
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 99.8 0.765 0.895 0.461 0.716 1.8 3.7
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 5DAZ 1.7 42.34 21771 1087 0.1592 0.1623 0.1961 0.1995 32.82
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 f_dihedral_angle_d 15.702 f_angle_d 0.833 f_chiral_restr 0.051 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1275 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing