7E48

Crystal structure of InhA in complex with 3-nitropropanoic acid inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6R9W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.5293Purified protein incubated with NADH and 3NP in 5% (w/v) ethanol, 5% (w/v) MPD, 200mM sodium chloride, 100mM Tris-HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
3.1160.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.39α = 90
b = 96.39β = 90
c = 139.5γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2018-01-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLRI BEAMLINE BL7.2W1.24SLRIBL7.2W

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
12.528.7699.90.0868.32.650117
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)
12.52.6499.90.422.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6R9W2.528.7650088245899.9160.1860.18470.219534.882
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]
0.0810.0410.081-0.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.568
r_dihedral_angle_4_deg17.598
r_dihedral_angle_3_deg13.82
r_dihedral_angle_1_deg6.139
r_lrange_it2.731
r_lrange_other2.696
r_scangle_it1.259
r_scangle_other1.259
r_mcangle_it1.256
r_mcangle_other1.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.568
r_dihedral_angle_4_deg17.598
r_dihedral_angle_3_deg13.82
r_dihedral_angle_1_deg6.139
r_lrange_it2.731
r_lrange_other2.696
r_scangle_it1.259
r_scangle_other1.259
r_mcangle_it1.256
r_mcangle_other1.256
r_angle_refined_deg1.173
r_angle_other_deg1.095
r_mcbond_it0.71
r_mcbond_other0.71
r_scbond_it0.701
r_scbond_other0.701
r_nbd_other0.216
r_symmetry_nbd_other0.174
r_nbd_refined0.17
r_nbtor_refined0.146
r_xyhbond_nbd_refined0.134
r_symmetry_xyhbond_nbd_refined0.115
r_symmetry_nbd_refined0.084
r_symmetry_nbtor_other0.075
r_chiral_restr0.038
r_gen_planes_refined0.003
r_bond_refined_d0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7953
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms214

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing