3HIS

Crystal structure of Saporin-L1 from Saponaria officinalis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529120% PEG2000MME, 0.1M sodium acetate, 0.4M potassium thiocyanate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2846.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.939α = 78.86
b = 53.058β = 65.62
c = 54.632γ = 80.65
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-10-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.97NSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.4951.8592.50.06911.82.676910
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.491.5494.30.5172.67835

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.495076828384292.40.210.2080.24RANDOM12.985
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]
0.57-0.18-0.28-0.160.5-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.449
r_dihedral_angle_4_deg16.276
r_dihedral_angle_3_deg12.36
r_dihedral_angle_1_deg5.318
r_scangle_it2.988
r_scbond_it1.809
r_angle_refined_deg1.117
r_mcangle_it1.033
r_mcbond_it0.589
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.449
r_dihedral_angle_4_deg16.276
r_dihedral_angle_3_deg12.36
r_dihedral_angle_1_deg5.318
r_scangle_it2.988
r_scbond_it1.809
r_angle_refined_deg1.117
r_mcangle_it1.033
r_mcbond_it0.589
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4030
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction