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Structure of Rivax: A Human Ricin Vaccine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AAI PDB entry 2AAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 290 30% Ammonium Sulfate, 50 mM Sodium Acetate pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.56 α = 90 b = 66.56 β = 90 c = 136.72 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 BRUKER SMART 6000 2007-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54188
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.14 68.36 98.5 0.0988 21.11 12.35 17731 17463 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.23 87.4 0.3993 4.39 6.13 1736
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2AAI 2.14 59.87 16508 878 98.42 0.21831 0.2165 0.2179 0.25361 0.2545 RANDOM 16.761
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.855 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 16.389 r_dihedral_angle_1_deg 4.618 r_scangle_it 1.589 r_angle_refined_deg 0.98 r_scbond_it 0.891 r_mcangle_it 0.661 r_mcbond_it 0.396 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.855 r_dihedral_angle_4_deg 17.172 r_dihedral_angle_3_deg 16.389 r_dihedral_angle_1_deg 4.618 r_scangle_it 1.589 r_angle_refined_deg 0.98 r_scbond_it 0.891 r_mcangle_it 0.661 r_mcbond_it 0.396 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.198 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2064 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 10
Software Software Software Name Purpose PROTEUM PLUS data collection AMoRE phasing REFMAC refinement SAINT data reduction SADABS data scaling