9OBO | pdb_00009obo

Crystal structure of Mycobacterium tuberculosis isocitrate lyase 2 fixed in the apo form with disulfide bonds

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	10% (w/v) PEG8000, 20% ethylene glycol, 0.1 M Tris/Bicine

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.7	α = 90
b = 170.864	β = 94.137
c = 104.373	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2023-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.954	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.6	49.546	99.8	0.076	0.041	0.995	10.3	4.4		110858

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	100		0.679	0.354	0.766	2.2	4.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.6	49.546	110816	5620	99.665	0.175	0.172	0.1769	0.2235	0.2273	RANDOM	72.271

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]
-0.046		-0.279	-1.141		1.215

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.946
r_dihedral_angle_3_deg	13.21
r_lrange_it	5.925
r_lrange_other	5.906
r_dihedral_angle_1_deg	5.772
r_dihedral_angle_2_deg	3.9
r_mcangle_it	3.256
r_mcangle_other	3.256
r_scangle_it	3.224
r_scangle_other	3.224
r_mcbond_it	1.889
r_mcbond_other	1.889
r_scbond_it	1.845
r_scbond_other	1.844
r_angle_refined_deg	0.873
r_angle_other_deg	0.302
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_refined	0.197
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.166
r_xyhbond_nbd_refined	0.149
r_nbd_other	0.133
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.042
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23416
Nucleic Acid Atoms
Solvent Atoms	715
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing