1ZJN

Human DNA Polymerase beta complexed with DNA containing an A-A mismatched primer terminus with dGTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BPYPDB ENTRY 1BPY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291PEG 3350, Sodium Acetate, Imidazole, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6553.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.1α = 90
b = 79.5β = 106.2
c = 55.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2003-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418

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
12.650991228711760-349.4
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)
12.62.6999.10.4263.31190

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BPY2.6130.391228711760121294.40.2280.2280.234RANDOM43.6
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]
9.65-1.03-6.55-3.1
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.3
c_angle_deg1.4
c_improper_angle_d1.12
c_bond_d0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d21.3
c_angle_deg1.4
c_improper_angle_d1.12
c_bond_d0.013
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2596
Nucleic Acid Atoms630
Solvent Atoms82
Heterogen Atoms35

Software

Software
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing