1XXX

Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	292	100 mM Tris-HCl, 28 % PEG 4000, 170 mM MgCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 94.79	α = 90
b = 87.37	β = 107.78
c = 139.85	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		2004-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 5.2R		ELETTRA	5.2R

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	2.28	99	99.7	0.085	27.98			99893		-3

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	2.28	2.32	95		0.192	12.53

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1O5K	2.28	30	99362	97308	1987	100	0.149	0.148	0.17	0.215	0.22	RANDOM	29.5

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]
-0.71		-1.07	1.44		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.971
r_dihedral_angle_4_deg	17.901
r_dihedral_angle_3_deg	13.805
r_dihedral_angle_1_deg	6.496
r_scangle_it	5.89
r_scbond_it	4.049
r_angle_refined_deg	1.628
r_mcangle_it	1.53
r_mcbond_it	0.943
r_nbtor_refined	0.31
r_nbd_refined	0.219
r_symmetry_vdw_refined	0.216
r_symmetry_hbond_refined	0.202
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.096
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_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	17072
Nucleic Acid Atoms
Solvent Atoms	1587
Heterogen Atoms	80

Software

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