2IYW

Shikimate kinase from Mycobacterium tuberculosis in complex with MgATP, open LID (conf. B)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		25%(W/V) PEG 3000, 100MM MES PH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.97	α = 90
b = 44.581	β = 109.7
c = 51.762	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	CCD	MARRESEARCH	MIRRORS	2006-08-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	1.85	19.47	98.3	0.098	10.86	3.55		14156

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	1.85	1.99	98.5		0.42	3.35	3.5

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 2IYV	1.85	19.47	13422	734	98.3	0.163	0.161	0.2	RANDOM	17.05

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]
0.62		0.64	-0.39		0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.55
r_dihedral_angle_4_deg	15.487
r_dihedral_angle_3_deg	12.395
r_scangle_it	5.389
r_dihedral_angle_1_deg	4.708
r_angle_other_deg	3.542
r_scbond_it	3.19
r_mcangle_it	2.002
r_angle_refined_deg	1.322
r_mcbond_it	1.12
r_symmetry_vdw_other	0.257
r_nbd_other	0.238
r_nbd_refined	0.218
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.151
r_symmetry_vdw_refined	0.14
r_symmetry_hbond_refined	0.131
r_nbtor_other	0.1
r_chiral_restr	0.066
r_bond_refined_d	0.01
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
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	1318
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	32

Software

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