2WB0 | pdb_00002wb0

2.1 resolution structure of the C-terminal domain of the human adenovirus 5 ssDNA binding protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ADTPDB ENTRY 1ADT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.8pH 5.8
Crystal Properties
Matthews coefficientSolvent content
2.4248.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.29α = 90
b = 76.66β = 90
c = 64.69γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
11.951598.60.0621.33.629937-3
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)
11.952.0599.30.324.53.4

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 1ADT1.9514.9527042143698.40.1870.1840.190.2450.24RANDOM26.45
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
r_dihedral_angle_2_deg38.183
r_dihedral_angle_4_deg18.744
r_dihedral_angle_3_deg18.681
r_dihedral_angle_1_deg6.221
r_scangle_it5.536
r_scbond_it3.577
r_mcangle_it2.323
r_angle_refined_deg2.25
r_mcbond_it1.355
r_chiral_restr0.282
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.183
r_dihedral_angle_4_deg18.744
r_dihedral_angle_3_deg18.681
r_dihedral_angle_1_deg6.221
r_scangle_it5.536
r_scbond_it3.577
r_mcangle_it2.323
r_angle_refined_deg2.25
r_mcbond_it1.355
r_chiral_restr0.282
r_bond_refined_d0.026
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms2471
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing