5W35

Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 1-nucleotide overhang


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7294100 mM Hepes pH 7.0, 6% PEG 4000, 5 mM SrCl2
Crystal Properties
Matthews coefficientSolvent content
2.6753.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.995α = 90
b = 210.414β = 108.6
c = 47.752γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2017-04-11MSINGLE 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
13.35099.8244.412200

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 REPLACEMENTTHROUGHOUT5W343.31351155062099.160.226170.223570.27857RANDOM
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]
4.63-1.43-9.384.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.184
r_dihedral_angle_3_deg15.911
r_dihedral_angle_4_deg14.783
r_long_range_B_refined10.271
r_long_range_B_other10.27
r_mcangle_it7.375
r_mcangle_other7.374
r_scangle_other6.698
r_dihedral_angle_1_deg5.855
r_mcbond_other4.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.184
r_dihedral_angle_3_deg15.911
r_dihedral_angle_4_deg14.783
r_long_range_B_refined10.271
r_long_range_B_other10.27
r_mcangle_it7.375
r_mcangle_other7.374
r_scangle_other6.698
r_dihedral_angle_1_deg5.855
r_mcbond_other4.422
r_mcbond_it4.421
r_scbond_it3.858
r_scbond_other3.855
r_angle_refined_deg1.111
r_angle_other_deg0.913
r_chiral_restr0.056
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms78
Solvent Atoms
Heterogen Atoms

Software

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