5W36

Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 6-nucleotide overhang


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W34 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6294100 mM sodium citrate pH 6.0, 5% w/v PEG 4000 and 5 mM SrCl2
Crystal Properties
Matthews coefficientSolvent content
2.7254.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.837α = 90
b = 210.936β = 106.78
c = 46.046γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0APS22-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
12.455096.2232.727849

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 REPLACEMENTTHROUGHOUT5W342.463526558125395.720.217750.215130.26915RANDOM
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]
3.01-1.2-2.80.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_3_deg17.301
r_dihedral_angle_4_deg16.644
r_long_range_B_refined7.578
r_long_range_B_other7.578
r_dihedral_angle_1_deg6.157
r_scangle_other5.232
r_mcangle_it4.907
r_mcangle_other4.906
r_scbond_it3.359
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.116
r_dihedral_angle_3_deg17.301
r_dihedral_angle_4_deg16.644
r_long_range_B_refined7.578
r_long_range_B_other7.578
r_dihedral_angle_1_deg6.157
r_scangle_other5.232
r_mcangle_it4.907
r_mcangle_other4.906
r_scbond_it3.359
r_scbond_other3.357
r_mcbond_it3.021
r_mcbond_other3.021
r_angle_refined_deg1.259
r_angle_other_deg0.954
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4932
Nucleic Acid Atoms42
Solvent Atoms47
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing