2IYT

Shikimate kinase from Mycobacterium tuberculosis in unliganded state, open LID (conf. A)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		170MM NA ACETATE, 15%(V/V) GLYCEROL, 25.5%(W/V) PEG 4000, 85MM TRIS-HCL PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
1.8	31.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.192	α = 90
b = 44.192	β = 90
c = 152.628	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC CCD	MIRRORS	2005-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	1.47	19.73	97.6	0.1	7.15	4.05		26142

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	1.47	1.51	98.7		0.72	2.04	4

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 2IYS	1.47	19.73	24844	1298	97.6	0.199	0.197	0.246	RANDOM	20.54

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]
-0.08			-0.08		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.553
r_dihedral_angle_4_deg	17.585
r_scangle_it	16.113
r_dihedral_angle_3_deg	14.959
r_scbond_it	14.15
r_mcangle_it	6.532
r_dihedral_angle_1_deg	5.165
r_mcbond_it	4.99
r_angle_other_deg	3.571
r_angle_refined_deg	1.766
r_symmetry_vdw_other	0.332
r_nbd_other	0.233
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.228
r_symmetry_hbond_refined	0.188
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.152
r_chiral_restr	0.117
r_nbtor_other	0.102
r_bond_refined_d	0.021
r_gen_planes_other	0.011
r_gen_planes_refined	0.009
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_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	1293
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling