5AB8

High resolution X-ray structure of the N-terminal truncated form (residues 1-11) of Mycobacterium tuberculosis HbN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IDRPDB ENTRY 1IDR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.62772.0 M NA-FORMATE, 0.1 M NA-ACETATE PH 4.6, T=277 K
Crystal Properties
Matthews coefficientSolvent content
2.1843.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.16α = 90
b = 43.16β = 90
c = 212.9γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.5353.2399.90.115.715.5189443
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.531.6199.60.45.815.9

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1IDR1.5333.071785196999.840.143840.140440.20917RANDOM27.522
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]
0.070.070.07-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.028
r_sphericity_free32.976
r_sphericity_bonded12.829
r_dihedral_angle_3_deg12.292
r_dihedral_angle_4_deg10.784
r_dihedral_angle_1_deg5.693
r_mcangle_it4.311
r_scbond_it4.204
r_mcbond_it3.902
r_mcbond_other3.834
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.028
r_sphericity_free32.976
r_sphericity_bonded12.829
r_dihedral_angle_3_deg12.292
r_dihedral_angle_4_deg10.784
r_dihedral_angle_1_deg5.693
r_mcangle_it4.311
r_scbond_it4.204
r_mcbond_it3.902
r_mcbond_other3.834
r_rigid_bond_restr3.353
r_angle_refined_deg1.508
r_angle_other_deg0.856
r_chiral_restr0.113
r_gen_planes_refined0.012
r_bond_refined_d0.01
r_gen_planes_other0.01
r_bond_other_d0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms871
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing