☰ Navigation Tabs
Atomic resolution structure of atratoxin-b, one short-chain neurotoxin from Naja atra
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ONJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 Tris_HCl, ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.86 35.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.463 α = 90 b = 48.463 β = 90 c = 44.133 γ = 90
Symmetry Space Group P 41 21 2
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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.916 CHESS F1
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 0.92 30 99.4 0.075 12.8 36907 36907
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) 0.92 0.94 92 0.21
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO THROUGHOUT 1onj 0.92 30 36907 36907 1850 99.4 0.1141 0.1328 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 9 415 584.62
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.149 s_zero_chiral_vol 0.095 s_approx_iso_adps 0.089 s_angle_d 0.04 s_from_restr_planes 0.0388 s_similar_adp_cmpnt 0.035 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 507 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SHELX model building SHELXL-97 refinement AMoRE phasing