6B5K

Mycobacterium tuberculosis RmlA in complex with Mg/dTTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H5S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729318 - 22% poly(ethylene glycol) 8000 and 100 mM MOPS
Crystal Properties
Matthews coefficientSolvent content
2.9758.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.403α = 90
b = 96.403β = 90
c = 151.924γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-06-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9794APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.65098.50.04955.75.989386
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.66970.1985.93.7

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 REPLACEMENTTHROUGHOUT1H5S1.65084972441498.410.196170.19460.22694RANDOM31.691
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]
0.470.47-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.43
r_dihedral_angle_4_deg16.49
r_dihedral_angle_3_deg15.082
r_dihedral_angle_1_deg7.285
r_long_range_B_refined6.581
r_long_range_B_other6.581
r_scangle_other5.423
r_mcangle_it4.433
r_mcangle_other4.432
r_scbond_it3.816
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.43
r_dihedral_angle_4_deg16.49
r_dihedral_angle_3_deg15.082
r_dihedral_angle_1_deg7.285
r_long_range_B_refined6.581
r_long_range_B_other6.581
r_scangle_other5.423
r_mcangle_it4.433
r_mcangle_other4.432
r_scbond_it3.816
r_scbond_other3.815
r_mcbond_other3.42
r_mcbond_it3.419
r_angle_refined_deg1.676
r_angle_other_deg0.834
r_chiral_restr0.208
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms4198
Nucleic Acid Atoms
Solvent Atoms349
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing