5F0S

Crystal structure of C-terminal domain of the human DNA primase large subunit with bound DNA template/RNA primer and manganese ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5F0Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7295Reservoir solution containe 0.18 M lithium sulfate, 50 mM sodium citrate, 2 mM TCEP, 0.1 M sodium malonate, 0.1 M Hepes-NaOH (pH 7.0), 19.7% PEG 8,000 and 0.02 M magnesium chloride. To exchange Mg to Mn crystals were soaked for 5 min in a reservoir solution containing 2 mM manganese chloride instead of magnesium chloride.
Crystal Properties
Matthews coefficientSolvent content
2.9257.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.753α = 90
b = 125.613β = 90
c = 83.69γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2015-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E DW1.5418

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
132089.90.1056.83.211834-1
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)
133.0576.90.4351.81.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5F0Q319.871181860789.20.2320.269RANDOM52.5
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]
0.25-0.820.56
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.1
c_scangle_it5.72
c_mcangle_it4.61
c_scbond_it4
c_mcbond_it2.81
c_improper_angle_d1.77
c_angle_deg1.5
c_bond_d0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3035
Nucleic Acid Atoms721
Solvent Atoms
Heterogen Atoms18

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling