Experiment: 1L4Y

CRYSTAL STRUCTURE OF SHIKIMATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MGADP AT 2.0 ANGSTROM RESOLUTION

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L4U	PDB ENTRY 1L4U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	288.2	PEG 4000, Magnesium Choloride, Sodium Chloride, ADENOSINE-5'-DIPHOSPHATE, SHIKIMIC ACID, Na-HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.2K

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.86	α = 90
b = 63.86	β = 90
c = 92.07	γ = 120

Symmetry
Space Group	P 32 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	ADSC QUANTUM 4	MIRROR	1999-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B	0.92000	NSLS	X9B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	27.65	99.4	0.039	0.056	26.6	5.88	15110	14820		-3	26.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	99.9		0.389	0.41	4.64	5.8	1461

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	Difference Fourier	THROUGHOUT	PDB ENTRY 1L4U	2	30	14820	14820	739	97.8	0.217	0.2199	0.252	0.2519	RANDOM	35.1

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]
3.76	-0.78		3.76		-7.52

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	20.2
c_scangle_it	4.31
c_scbond_it	3.01
c_mcangle_it	2.87
c_mcbond_it	1.99
c_angle_deg	1.2
c_improper_angle_d	0.81
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1226
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms	33

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing