4I9L

Crystal structure of the D714A mutant of RB69 DNA polymerase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IH7PDB ENTRY 1IH7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.61.65 M AMMONIUM SULPHATE, 0.01 M MAGNESIUM CHLORIDE, 0.05 M SODIUM CITRATE DIHYDROGEN, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
4.572.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.875α = 90
b = 199.369β = 90
c = 80.822γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-06-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X12CNSLSX12C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.65099.50.140.1415.26.259560
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.71000.8290.8292.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1IH72.633.240.0952147173286.80.2160.2140.249
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]
-1.58957.7354-6.1459
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.806
f_angle_d1.016
f_chiral_restr0.068
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7368
Nucleic Acid Atoms
Solvent Atoms220
Heterogen Atoms38

Software

Software
Software NamePurpose
CBASSdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling