7E48 | pdb_00007e48

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6R9W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	8.5	293	Purified 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 coefficient	Solvent content
3.11	60.5

Crystal Data

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

Symmetry
Space Group	P 32

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MAR CCD 165 mm		2018-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLRI BEAMLINE BL7.2W	1.24	SLRI	BL7.2W

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	28.76	99.9	0.086	8.3	2.6		50117

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.64	99.9		0.42	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6R9W	2.5	28.76	50088	2458	99.916	0.186	0.1847	0.19	0.2195	0.23	34.882

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]
0.081	0.041		0.081		-0.263

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.568
r_dihedral_angle_4_deg	17.598
r_dihedral_angle_3_deg	13.82
r_dihedral_angle_1_deg	6.139
r_lrange_it	2.731
r_lrange_other	2.696
r_scangle_it	1.259
r_scangle_other	1.259
r_mcangle_it	1.256
r_mcangle_other	1.256
r_angle_refined_deg	1.173
r_angle_other_deg	1.095
r_mcbond_it	0.71
r_mcbond_other	0.71
r_scbond_it	0.701
r_scbond_other	0.701
r_nbd_other	0.216
r_symmetry_nbd_other	0.174
r_nbd_refined	0.17
r_nbtor_refined	0.146
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbd_refined	0.084
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.038
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7953
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	214

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing