8X5S

Crystal structure of shikimate kinase of Mycobacterium tuberculosis complex with shikimate-3-phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2IYX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 M Ammonium sulphate 0.1 M Sodium acetate trihydrate pH - 4.6 30% PEG 2000

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.424	α = 90
b = 59.424	β = 90
c = 102.25	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	273	PIXEL	DECTRIS PILATUS 6M		2022-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.96546	ESRF	BM30A

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.72	46.011	96	0.063	0.067	0.022	0.99	18.8	9.1		21710			29.5

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	1.72	1.756	100		1.072	0.369	0.913		9.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2IYX	1.726	46.011	21704	1144	95.98	0.179	0.1761	0.2222	33.05

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]
-0.003	-0.002		-0.003		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.407
r_dihedral_angle_3_deg	13.03
r_dihedral_angle_2_deg	11.865
r_lrange_it	11.305
r_lrange_other	11.262
r_scangle_it	7.24
r_scangle_other	7.085
r_dihedral_angle_1_deg	5.482
r_scbond_it	4.884
r_scbond_other	4.624
r_mcangle_other	4.458
r_mcangle_it	4.456
r_mcbond_it	3.14
r_mcbond_other	3.112
r_angle_refined_deg	1.747
r_angle_other_deg	0.594
r_symmetry_nbd_refined	0.347
r_nbd_refined	0.246
r_nbd_other	0.211
r_xyhbond_nbd_refined	0.201
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.195
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_xyhbond_nbd_other	0.109
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1252
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	36

Software

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