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Ricin A-chain variant 1-33/44-198 with engineered disulfide bond
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BJG PDB entry 3BJG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 290 Protein buffer: 50mM MES pH 6.4, 200mM NaCl
Crystallization Solution: 0.17M Ammonium Sulfate, 25.5% w/v PEG 4000, 15% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.493 α = 90 b = 72.307 β = 90 c = 94.208 γ = 90
Symmetry Space Group I 2 2 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 2009-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54
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 2.28 57.36 100 0.098 19.05 16.01 8335 8333 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.38 100 5.52 11.85 979
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 3BJG 2.28 57.36 7938 385 99.89 0.21511 0.21359 0.2128 0.2455 0.2421 RANDOM 18.408
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] -0.51 -0.6 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.943 r_dihedral_angle_4_deg 23.046 r_dihedral_angle_3_deg 17.311 r_dihedral_angle_1_deg 4.773 r_scangle_it 2.705 r_scbond_it 1.577 r_mcangle_it 1.162 r_angle_refined_deg 1.121 r_mcbond_it 0.607 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.943 r_dihedral_angle_4_deg 23.046 r_dihedral_angle_3_deg 17.311 r_dihedral_angle_1_deg 4.773 r_scangle_it 2.705 r_scbond_it 1.577 r_mcangle_it 1.162 r_angle_refined_deg 1.121 r_mcbond_it 0.607 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1361 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 5
Software Software Software Name Purpose PROTEUM PLUS data collection AMoRE phasing REFMAC refinement SAINT data reduction SADABS data scaling