8CIX

DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with Griselimycin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4K3L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.72930.36 M CaCl2 0.13 M MgCl2 0.24 M Na Acetate 8.3 % (v/v) Glycerol 12.2 % (w/v) PEG 3350 0.1 M HEPES/NaOH 7.7 Cryoprotection: 10 % (v/v) (2R,3R)-2,3-butanediol.
Crystal Properties
Matthews coefficientSolvent content
2.7755.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.936α = 90
b = 150.561β = 90
c = 71.594γ = 90
Symmetry
Space GroupC 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.7675.281000.0840.0880.024117.913.445185
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.861001.031.0690.2880.90213.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.7651.881.3545163242099.950.18010.17870.2053
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.747
f_angle_d1.035
f_chiral_restr0.062
f_bond_d0.01
f_plane_restr0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2793
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms113

Software

Software
Software NamePurpose
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement