1ZJ8

Structure of Mycobacterium tuberculosis NirA protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5293PEG 4000, tris-HCl, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.345.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.257α = 90
b = 115.355β = 90
c = 114.697γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.085MAX III711

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
12.8451000.10917.76.32821855.37
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)
12.82.951000.4693.56.34049

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GEP2.830.65257272672014361000.218660.218660.214690.29203RANDOM43.728
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]
-1.7-1.272.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.462
r_dihedral_angle_3_deg17.909
r_dihedral_angle_4_deg17.465
r_dihedral_angle_1_deg6.504
r_angle_refined_deg1.542
r_scangle_it1.474
r_scbond_it0.924
r_angle_other_deg0.873
r_mcangle_it0.864
r_mcbond_it0.775
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.462
r_dihedral_angle_3_deg17.909
r_dihedral_angle_4_deg17.465
r_dihedral_angle_1_deg6.504
r_angle_refined_deg1.542
r_scangle_it1.474
r_scbond_it0.924
r_angle_other_deg0.873
r_mcangle_it0.864
r_mcbond_it0.775
r_symmetry_vdw_other0.244
r_symmetry_vdw_refined0.24
r_symmetry_hbond_refined0.226
r_nbd_refined0.218
r_nbd_other0.188
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.159
r_mcbond_other0.102
r_nbtor_other0.086
r_xyhbond_nbd_other0.079
r_chiral_restr0.077
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8632
Nucleic Acid Atoms
Solvent Atoms22
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing