4QWC

Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus in Comples with DNA and L-DCDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FO3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729816% PEG 3350, 0.1 M HEPES (PH 7.0), 100MM CALCIUM ACETATE, 2.5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.7254.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.44α = 90
b = 101.93β = 90
c = 105.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.449.2299.341845
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)
12.42.491000.8922.810

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 REPLACEMENTTHROUGHOUT4FO32.446.4639665211099.160.229830.227280.27705RANDOM70.557
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]
-0.470.30.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.816
r_dihedral_angle_3_deg18.791
r_dihedral_angle_4_deg14.17
r_dihedral_angle_1_deg5.835
r_mcangle_it3.587
r_scbond_it2.173
r_mcbond_it2.109
r_mcbond_other2.109
r_angle_other_deg1.239
r_angle_refined_deg1.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.816
r_dihedral_angle_3_deg18.791
r_dihedral_angle_4_deg14.17
r_dihedral_angle_1_deg5.835
r_mcangle_it3.587
r_scbond_it2.173
r_mcbond_it2.109
r_mcbond_other2.109
r_angle_other_deg1.239
r_angle_refined_deg1.237
r_chiral_restr0.074
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5504
Nucleic Acid Atoms1108
Solvent Atoms175
Heterogen Atoms101

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling