2YIZ

X-ray structure of Mycobacterium tuberculosis Dodecin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V21	PDB ENTRY 2V21

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		10 MM CO CL2, 100 MM NAOAC PH 5.0, 200 MM HEXANEDIOL.

Crystal Properties
Matthews coefficient	Solvent content
3.18	61.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.302	α = 90
b = 94.302	β = 90
c = 230.907	γ = 120

Symmetry
Space Group	H 3 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	MARRESEARCH MX-300		2007-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A		EMBL/DESY, HAMBURG	BW7A

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	1.7	14.91	99.7	0.05	24.8	11.1		43832		-3	26.7

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	1.7	1.79	100		0.78	3.3	11.1

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 2V21	1.7	14.91	42659	1084	99.76	0.17261	0.17198	0.19743	RANDOM	27.99

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]
-0.3	-0.15		-0.3		0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.777
r_dihedral_angle_4_deg	14.867
r_dihedral_angle_3_deg	12.059
r_dihedral_angle_1_deg	6.61
r_scangle_it	3.642
r_scbond_it	2.134
r_mcangle_it	1.504
r_angle_refined_deg	1.342
r_mcbond_it	0.831
r_angle_other_deg	0.788
r_mcbond_other	0.209
r_chiral_restr	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_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	2084
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	204

Software

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