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Crystal structure of Dendroaspis polylepis mambalgin-1 wild-type in P41212 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 7 293 Protein: 5 mg/mL in 0.050 M Na Acetate, pH 5.5
Precipitant: 30% PEG600, 0.2 M Imidazole Malate, pH 7.0.
Cryoprotectant: 40% CryoSol SM5, 30% PEG 600, 0.1 M mixed (Na acetate, ADA, Bicine) pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.68 26.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.8 α = 90 b = 46.8 β = 90 c = 80.56 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 PIXEL DECTRIS PILATUS 6M automatic data collection on ESRF Massif1 ID30A-1 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 1.95 46.8 99.9 0.183 0.171 9.66 7.5 6985 6981 -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 1.95 2 100 1.67 1.19 7.94
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 5DO6 1.95 40.467 1.35 6979 349 99.91 0.1949 0.192 0.197 0.2459 0.2413 Random selection
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 16.1 f_angle_d 1.991 f_chiral_restr 0.112 f_bond_d 0.025 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 902 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing XSCALE data scaling MxCuBE data collection Coot model building XDS data reduction