2IRX

Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D with GTP and Manganese.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52850.1M Na Hepes, 0.01M MnCl2, 10%(v/v) iso-propanol, 20% PEG 4000, 0.01M GTP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.1943.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.557α = 90
b = 75.532β = 90
c = 89.518γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2006-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54180

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
11.834.7998.40.0590.06726.5927079-3.721.30639
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)
11.81.989.10.4080.4782.95.33490

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.834.792702625666136098.40.166460.164180.20943RANDOM15.446
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]
0.39-0.01-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.435
r_dihedral_angle_4_deg21.39
r_dihedral_angle_3_deg14.203
r_dihedral_angle_1_deg6.007
r_scangle_it3.017
r_scbond_it1.996
r_angle_refined_deg1.429
r_mcangle_it1.216
r_mcbond_it0.795
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.435
r_dihedral_angle_4_deg21.39
r_dihedral_angle_3_deg14.203
r_dihedral_angle_1_deg6.007
r_scangle_it3.017
r_scbond_it1.996
r_angle_refined_deg1.429
r_mcangle_it1.216
r_mcbond_it0.795
r_nbtor_refined0.299
r_nbd_refined0.202
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.155
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2164
Nucleic Acid Atoms
Solvent Atoms327
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing