5ZQN

Crystal structure of Mycobacterium tuberculosis HisB in complex with a ligand


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PEG 1500, sodium citrate tribasic dehydrate, tris HCl
Crystal Properties
Matthews coefficientSolvent content
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.715α = 90
b = 112.715β = 90
c = 112.715γ = 90
Symmetry
Space GroupP 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2017-04-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.83599.90.10121.0813.723350
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.861002.3910.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4LOM1.828.223350117999.90.1550.187RANDOM22.79
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.72
r_dihedral_angle_4_deg17.512
r_dihedral_angle_3_deg14.414
r_dihedral_angle_1_deg6.983
r_scangle_it4.568
r_scangle_other4.566
r_scbond_it3.035
r_scbond_other3.033
r_mcangle_it2.494
r_mcangle_other2.494
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.72
r_dihedral_angle_4_deg17.512
r_dihedral_angle_3_deg14.414
r_dihedral_angle_1_deg6.983
r_scangle_it4.568
r_scangle_other4.566
r_scbond_it3.035
r_scbond_other3.033
r_mcangle_it2.494
r_mcangle_other2.494
r_angle_refined_deg1.709
r_mcbond_it1.696
r_mcbond_other1.694
r_angle_other_deg1.414
r_nbd_refined0.223
r_xyhbond_nbd_refined0.211
r_nbd_other0.196
r_nbtor_refined0.158
r_chiral_restr0.077
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbtor_other
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_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1465
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms18

Software

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