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Structure of alpha-elapitoxin-Dpp2d isolated from Black Mamba (Dendroaspis polylepis) venom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NTN PDB ENTRY 1NTN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 protein was dissolved in 2mM HCl, 5 mg/mL. reservoir: 0.1M TRIS-HCL, 2% (v/v) dioxane, 65% (v/v) 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.595 α = 90 b = 38.27 β = 90 c = 39.419 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU SATURN 944 2012-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.54
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 1.7 27.46 92.85 0.045 27.2 5.53 121995 22047 23.903
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 1.7 1.744 74.79 0.483 1.9 2.16
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-Factor (All) 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 1NTN 1.7 27.46 22047 15981 848 92.85 0.19916 0.19916 0.1978 0.2059 0.22371 0.2251 RANDOM 23.903
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] -0.07 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_4_deg 12.195 r_long_range_B_refined 7.315 r_dihedral_angle_1_deg 7.145 r_long_range_B_other 7.015 r_scangle_other 5.292 r_scbond_it 3.486 r_scbond_other 3.483 r_mcangle_it 3.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.021 r_dihedral_angle_3_deg 12.418 r_dihedral_angle_4_deg 12.195 r_long_range_B_refined 7.315 r_dihedral_angle_1_deg 7.145 r_long_range_B_other 7.015 r_scangle_other 5.292 r_scbond_it 3.486 r_scbond_other 3.483 r_mcangle_it 3.452 r_mcangle_other 3.45 r_mcbond_it 2.508 r_mcbond_other 2.503 r_angle_refined_deg 2.267 r_angle_other_deg 0.956 r_chiral_restr 0.145 r_bond_refined_d 0.024 r_gen_planes_refined 0.012 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1034 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling