3L21

The crystal structure of a dimeric mutant of dihydrodipicolinate synthase (DAPA, RV2753C) from Mycobacterium Tuberculosis - DHDPS-A204R

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XXX	Wild-type M. tuberculosis DHDPS, PDB ENTRY 1XXX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	2.0M ammonium sulfate, 100mM sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 188.83	α = 90
b = 188.83	β = 90
c = 130.43	γ = 90

Symmetry
Space Group	P 41 21 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	MARMOSAIC 225 mm CCD		2008-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3	1.000	MAX II	I911-3

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	99	99.2	0.118	14.1	4.8	157209	155951

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)
	2	2.052	97.6		0.589	2.5	4.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Wild-type M. tuberculosis DHDPS, PDB ENTRY 1XXX	2.1	28.51	151456	130491	4197	98.54	0.17926	0.17849	0.20389	RANDOM	23.177

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]
-0.55			-0.55		1.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.004
r_dihedral_angle_4_deg	17.352
r_dihedral_angle_3_deg	13.573
r_dihedral_angle_1_deg	6.152
r_scangle_it	4.108
r_scbond_it	3.108
r_mcangle_it	1.607
r_angle_refined_deg	1.52
r_mcbond_it	1.043
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.268
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.155
r_symmetry_hbond_refined	0.141
r_chiral_restr	0.095
r_bond_refined_d	0.015
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_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	12875
Nucleic Acid Atoms
Solvent Atoms	1596
Heterogen Atoms	293

Software

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