2RDI

Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JX4PDB ENTRY 1JX4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.929420% PEG3350, 0.2M lithium nitrate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.5852.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.927α = 90
b = 51.069β = 98.08
c = 86.026γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2005-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.923093.80.04316.833079628887-137.479
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)
11.921.9590.60.5072.51393

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB ENTRY 1JX41.9220.35-1293122793412171000.2070.2070.2050.247RANDOM46.44
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.645
r_dihedral_angle_4_deg19.366
r_dihedral_angle_3_deg17.554
r_dihedral_angle_1_deg6.629
r_scangle_it2.815
r_scbond_it1.849
r_angle_refined_deg1.427
r_mcangle_it1.116
r_mcbond_it0.738
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.645
r_dihedral_angle_4_deg19.366
r_dihedral_angle_3_deg17.554
r_dihedral_angle_1_deg6.629
r_scangle_it2.815
r_scbond_it1.849
r_angle_refined_deg1.427
r_mcangle_it1.116
r_mcbond_it0.738
r_nbtor_refined0.303
r_nbd_refined0.208
r_symmetry_vdw_refined0.207
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.169
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2701
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms13

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing