3EKL | pdb_00003ekl

Structural Characterization of tetrameric Mycobacterium tuberculosis fructose 1,6-bisphosphate aldolase - substrate binding and catalysis mechanism of a class IIa bacterial aldolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B57	Homology model derived from PDB ENTRY 1B57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	298	26% PEG 300, 0.1 NaAcetate pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.07	69.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.285	α = 90
b = 120.227	β = 90
c = 164.823	γ = 90

Symmetry
Space Group	I 2 2 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		2008-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

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	1.51	97.1	96.5			91761	91761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.51	1.56	89.6

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	Homology model derived from PDB ENTRY 1B57	1.51	97.1	91755	91755	4602	95.99	0.16674	0.16623	0.23	0.17637	0.23	RANDOM	22.063

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]
0.79			-0.5		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.335
r_dihedral_angle_4_deg	18.553
r_dihedral_angle_3_deg	11.39
r_dihedral_angle_1_deg	9.437
r_scangle_it	2.361
r_scbond_it	1.473
r_angle_refined_deg	1.21
r_mcangle_it	0.741
r_mcbond_it	0.42
r_nbtor_refined	0.305
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.175
r_xyhbond_nbd_refined	0.107
r_symmetry_hbond_refined	0.087
r_chiral_restr	0.086
r_metal_ion_refined	0.046
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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_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	2718
Nucleic Acid Atoms
Solvent Atoms	505
Heterogen Atoms	23

Software

Software
Software Name	Purpose
SERGUI	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling