2RDJ

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
1729410-15% PEG3350, 0.2M calcium acetate, 0.1M HEPES pH 7.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.754.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.993α = 90
b = 102.51β = 90
c = 106.109γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateMSINGLE 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
12.23097.50.05518.12.853280519482
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)
12.22.2499.70.362.12513

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 1JX42.224.112519245192426601000.2210.2210.210.256RANDOM45.17
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]
2.55-1.66-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.202
r_dihedral_angle_4_deg16.448
r_dihedral_angle_3_deg15.631
r_dihedral_angle_1_deg5.554
r_scangle_it2.756
r_scbond_it1.744
r_angle_refined_deg1.502
r_mcangle_it1.115
r_mcbond_it0.678
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.202
r_dihedral_angle_4_deg16.448
r_dihedral_angle_3_deg15.631
r_dihedral_angle_1_deg5.554
r_scangle_it2.756
r_scbond_it1.744
r_angle_refined_deg1.502
r_mcangle_it1.115
r_mcbond_it0.678
r_nbtor_refined0.303
r_nbd_refined0.2
r_xyhbond_nbd_refined0.154
r_metal_ion_refined0.152
r_symmetry_vdw_refined0.151
r_symmetry_hbond_refined0.136
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5486
Nucleic Acid Atoms1202
Solvent Atoms305
Heterogen Atoms31

Software

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