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Crystal structure of AdTx1 (rho-Da1a) from eastern green mamba (Dendroaspis angusticeps)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FF4 PDB ENTRY 1FF4 without loop 1 tip
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Lyophilization 8 273 Crystallization during lyophilization due to increased concentration and low temperature. Cryoconditions: 27% PEG8K, 15% MPEG550, 10% glycerol, 0.09 M Tris-HCl, pH 8.0, Lyophilization, temperature 273K
Crystal Properties Matthews coefficient Solvent content 1.82 32.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.37 α = 90 b = 37.37 β = 90 c = 66.05 γ = 120
Symmetry Space Group P 31 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 ADSC QUANTUM 4 mirrors 2010-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.9334 ESRF ID14-1
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 32.36 93.9 0.171 0.16 11.43 8.44 4193 3937 -4 25.325
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.07 69.1 1.088 0.947 1.12 2.89 660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 1FF4 without loop 1 tip 1.951 32.36 -3 3937 3738 197 93.89 0.17545 0.17445 0.17033 0.1738 0.25188 0.265 RANDOM 25.704
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] 1.63 1.63 1.63 -5.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_3_deg 14.462 r_sphericity_bonded 12.756 r_dihedral_angle_4_deg 9.449 r_dihedral_angle_1_deg 7.225 r_rigid_bond_restr 5.042 r_angle_refined_deg 1.648 r_angle_other_deg 1.233 r_chiral_restr 0.08 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_3_deg 14.462 r_sphericity_bonded 12.756 r_dihedral_angle_4_deg 9.449 r_dihedral_angle_1_deg 7.225 r_rigid_bond_restr 5.042 r_angle_refined_deg 1.648 r_angle_other_deg 1.233 r_chiral_restr 0.08 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 505 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 18
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling