3FSX | pdb_00003fsx

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	190 mM magnesium acetate tetrahydrate, 100 mM sodium cacodylate pH 6.5, 10 %(w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 216.99	α = 90
b = 216.99	β = 90
c = 216.99	γ = 90

Symmetry
Space Group	I 21 3

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	MARMOSAIC 225 mm CCD		2008-06-13	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.0000	MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.15	37.21	100		10.4	91741	91416		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19	99.7			8.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.15	30	90536	90238	1126	99.67	0.16856	0.16793	0.17	0.21945	0.22	RANDOM	30.215

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.299
r_dihedral_angle_4_deg	19.042
r_dihedral_angle_3_deg	14.173
r_scangle_it	6.976
r_dihedral_angle_1_deg	6.417
r_scbond_it	4.645
r_mcangle_it	1.966
r_angle_refined_deg	1.724
r_mcbond_it	1.075
r_chiral_restr	0.119
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10866
Nucleic Acid Atoms
Solvent Atoms	570
Heterogen Atoms	53

Software

Software
Software Name	Purpose
MxCuBE	data collection
Auto-Rickshaw	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling