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Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P21 space group.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DO6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 protein: 5 mg/mL in 0.550 M Na Acetate pH 5.5
precipitant: 18% PEG4K, 3% MPD, 3% 1,4-dioxane, .188 M Imidazole Malate, pH 6
cryoprotectant:: CrySol-SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine), pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.74 29.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.03 α = 90 b = 50.24 β = 93.38 c = 46.88 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 2M Compound Refractive Lens Fully automatic data collection 2015-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965 ESRF MASSIF-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 1.8 46.796 93.8 0.063 0.052 13.77 2.7 15969 15969 -3
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 1.8 1.91 84.7 0.257 4.35 2.77
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 5DO6 1.8 38.96 15332 807 95.3 0.17662 0.17406 0.22433 0.2331 RANDOM 27.705
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] 3.11 0.22 -1.22 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.855 r_dihedral_angle_4_deg 21.029 r_dihedral_angle_3_deg 17.159 r_long_range_B_refined 9.462 r_long_range_B_other 9.446 r_dihedral_angle_1_deg 7.997 r_scangle_other 5.76 r_mcangle_other 4.125 r_mcangle_it 4.123 r_scbond_it 3.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.855 r_dihedral_angle_4_deg 21.029 r_dihedral_angle_3_deg 17.159 r_long_range_B_refined 9.462 r_long_range_B_other 9.446 r_dihedral_angle_1_deg 7.997 r_scangle_other 5.76 r_mcangle_other 4.125 r_mcangle_it 4.123 r_scbond_it 3.723 r_scbond_other 3.715 r_mcbond_it 2.696 r_mcbond_other 2.676 r_angle_other_deg 2.375 r_angle_refined_deg 2.065 r_chiral_restr 0.103 r_bond_refined_d 0.019 r_bond_other_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.011 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 1804 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building