4BQS

Crystal structure of Mycobacterium tuberculosis shikimate kinase in complex with ADP and a shikimic acid derivative.

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G1K	PDB ENTRY 2G1K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	291	VAPOR DIFUSION, SITTING DROP, 20% (W/V) PEG 3350, 500 MM LICL AND 100 MM TRIS.HCL PH 7.8, ATP, SHIKIMIC ACID DERIVATIVE, TEMPERATURE 291 K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.653	α = 90
b = 60.959	β = 95.44
c = 89.976	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 PILATUS	MIRRORS	2013-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02		Diamond	I02

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	2.15	28.85	95.6	0.08	11.1	3.3		22876		2	21

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	2.15	2.27	79.4		0.34	3.5	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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2G1K	2.15	28.87	21698	1165	95.27	0.17554	0.1723	0.23506	RANDOM	30.371

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]
1.07		2.91	-0.79		-0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.213
r_dihedral_angle_4_deg	20.378
r_dihedral_angle_3_deg	15.562
r_scangle_it	6.953
r_dihedral_angle_1_deg	5.853
r_scbond_it	5.812
r_mcangle_it	3.777
r_mcbond_it	2.467
r_angle_refined_deg	1.747
r_angle_other_deg	0.856
r_mcbond_other	0.579
r_symmetry_vdw_refined	0.347
r_nbd_refined	0.239
r_nbtor_refined	0.182
r_nbd_other	0.169
r_symmetry_vdw_other	0.163
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.149
r_xyhbond_nbd_other	0.145
r_chiral_restr	0.085
r_nbtor_other	0.084
r_symmetry_hbond_other	0.018
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_metal_ion_refined
r_metal_ion_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3774
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	126

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing