9RJG | pdb_00009rjg

Structure of Mycobacterium tuberculosis InhA in complex with pyridomycin (compound 1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8OTL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.1293InhA at 4-8 mg/ml 30% (v/v) PEG 300 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
2.2445.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.23α = 90
b = 82.5β = 95.89
c = 188.41γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2024-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.96770ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.71162.47298.80.09210.10030.03940.99812.646.34162423
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.7111.74199.50.89520.97390.37930.6372.176.528079

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.71162.47162416812198.70.17360.17240.16830.19440.1897RANDOM30.26
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]
1.59891.4515-1.4251-0.1737
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion14.15
t_omega_torsion3.66
t_angle_deg0.94
t_bond_d0.009
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11491
Nucleic Acid Atoms
Solvent Atoms1118
Heterogen Atoms244

Software

Software
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
XSCALEdata scaling
TRUNCATEdata processing
PHASERphasing
Cootmodel building
XDSdata reduction