4A09

Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EI1PDB ENTRY 3EI1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.3100 MM MES, 15 MM NAOH, 21% PEG 200, pH 5.3
Crystal Properties
Matthews coefficientSolvent content
3.2462.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.65α = 90
b = 122.94β = 90
c = 154.2γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2010-11-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
13.15099.80.13167.3390922
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)
13.13.299.60.584.57.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3EI13.148.273713719551000.248330.245190.240.307530.3RANDOM56.702
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]
-1.9-2.964.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.784
r_dihedral_angle_3_deg16.538
r_dihedral_angle_4_deg15.282
r_dihedral_angle_1_deg5.194
r_angle_refined_deg0.996
r_scangle_it0.772
r_mcangle_it0.476
r_scbond_it0.394
r_mcbond_it0.262
r_chiral_restr0.063
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11485
Nucleic Acid Atoms605
Solvent Atoms22
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing