5DAZ

Crystal structure of Scabin, a mono-ADP-ribosyltransferase from Streptomyces scabies


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CB4PDB entry 2CB4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298100 mM MES, pH 6.5, 15% PEG400
Crystal Properties
Matthews coefficientSolvent content
2.2946.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.787α = 90
b = 61.075β = 99.64
c = 37.812γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-04-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.979CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.4543.27394.40.0420.04818.8133118-326.76
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.451.54810.7640.8762.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB entry 2CB41.4543.2731437165594.750.16680.16490.2021RANDOM27.961
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]
-0.180.50.04-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.384
r_dihedral_angle_4_deg19.897
r_dihedral_angle_3_deg13.359
r_dihedral_angle_1_deg8.317
r_mcangle_it3.538
r_angle_refined_deg2.81
r_mcbond_it2.346
r_mcbond_other2.335
r_angle_other_deg1.366
r_chiral_restr0.166
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.384
r_dihedral_angle_4_deg19.897
r_dihedral_angle_3_deg13.359
r_dihedral_angle_1_deg8.317
r_mcangle_it3.538
r_angle_refined_deg2.81
r_mcbond_it2.346
r_mcbond_other2.335
r_angle_other_deg1.366
r_chiral_restr0.166
r_bond_refined_d0.033
r_gen_planes_refined0.017
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1313
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing