2IRU

Crystal Structure of the Polymerase Domain from Mycobacterium tuberculosis Ligase D


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.728520% PEG 3350, 0.2 M Mg acetate, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties
Matthews coefficientSolvent content
2.2745.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.053α = 90
b = 75.796β = 92.68
c = 96.1γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2006-08-04MSINGLE 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
11.6520.3790.10.070.02923.76.463571-3.720.1
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)
11.651.7474.80.2350.12933.67663

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 REPLACEMENTTHROUGHOUT1.6520.376355060313323789.860.192730.19020.23896RANDOM15.758
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]
0.65-0.12-0.21-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.814
r_dihedral_angle_4_deg19.88
r_dihedral_angle_3_deg13.589
r_dihedral_angle_1_deg6.097
r_scangle_it3.382
r_scbond_it2.269
r_angle_refined_deg1.478
r_mcangle_it1.43
r_mcbond_it0.924
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.814
r_dihedral_angle_4_deg19.88
r_dihedral_angle_3_deg13.589
r_dihedral_angle_1_deg6.097
r_scangle_it3.382
r_scbond_it2.269
r_angle_refined_deg1.478
r_mcangle_it1.43
r_mcbond_it0.924
r_nbtor_refined0.302
r_xyhbond_nbd_refined0.26
r_symmetry_hbond_refined0.247
r_nbd_refined0.215
r_symmetry_vdw_refined0.198
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.007
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 Atoms4344
Nucleic Acid Atoms
Solvent Atoms663
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing