2IYZ

Shikimate kinase from Mycobacterium tuberculosis in complex with shikimate-3-phosphate and ADP

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		200MM NH4F,20%(W/V) PEG 3350, pH 8.00

Crystal Properties
Matthews coefficient	Solvent content
2.5	51.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.61	α = 90
b = 59.61	β = 90
c = 102.911	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	100	CCD	MARRESEARCH	MIRRORS	2006-02-26	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	2.3	19.49	95.8	0.09	6.69	1.96		9427

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	2.3	2.36	98.7		0.3	2.79	1.9

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 2IYX	2.3	19.49	8978	449	95.8	0.193	0.191	0.242	RANDOM	24.47

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]
1.25	0.63		1.25		-1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.065
r_dihedral_angle_3_deg	15.778
r_dihedral_angle_4_deg	14.025
r_dihedral_angle_1_deg	5.087
r_scangle_it	3.214
r_scbond_it	2.018
r_angle_refined_deg	1.526
r_mcangle_it	1.185
r_mcbond_it	1.106
r_angle_other_deg	0.815
r_symmetry_vdw_other	0.244
r_nbd_refined	0.214
r_nbd_other	0.193
r_symmetry_hbond_refined	0.193
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.168
r_symmetry_vdw_refined	0.148
r_nbtor_other	0.083
r_chiral_restr	0.072
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	1247
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	43

Software

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