4IMV

Ricin A-chain variant 1-33/44-198 with engineered disulfide bond, R48C/T77C/D75N


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42900.17 M Ammonium Sulfate, 25.5% (w/v) Peg 4000, 15% Glycerol , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.0640.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.585α = 90
b = 72.336β = 90
c = 94.694γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDBruker Platinum 1352012-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR-H1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2557.4899.10.119113.016.8887218640320.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3491.60.41913.624.18939

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.2557.4838721823340599.050.21560.214310.24229RANDOM23.598
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]
-0.5-0.941.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.313
r_dihedral_angle_4_deg23.637
r_dihedral_angle_3_deg13.653
r_angle_other_deg3.614
r_dihedral_angle_1_deg3.177
r_angle_refined_deg1.369
r_chiral_restr0.083
r_bond_refined_d0.015
r_gen_planes_other0.012
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.313
r_dihedral_angle_4_deg23.637
r_dihedral_angle_3_deg13.653
r_angle_other_deg3.614
r_dihedral_angle_1_deg3.177
r_angle_refined_deg1.369
r_chiral_restr0.083
r_bond_refined_d0.015
r_gen_planes_other0.012
r_gen_planes_refined0.007
r_sphericity_bonded
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_bond_other_d
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1317
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms5

Software

Software
Software NamePurpose
PROTEUM PLUSdata collection
AMoREphasing
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling