3KGF | pdb_00003kgf

The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with phenylalanine and tryptophan

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B7O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	20mM BTP, 150mM NaCl, 0.5mM TCEP, 0.005%(v/v) Thesit, 0.2mM PEP, 0.1mM MnCl2, 0.1M Na HEPES, 0.8M NaK phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 204.537	α = 90
b = 204.537	β = 90
c = 66.462	γ = 120

Symmetry
Space Group	P 32 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	RIGAKU RAXIS IV	Osmic Blue Mirrors	2005-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.542

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	39.5	98.2	0.064	8.2	2.07	105425	105425			37.5

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	2.07	87.2		0.381	2.1	2.38	10487

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 (All)	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	2b7o	2	32.67	105110	105110	5245	97.91	0.16423	0.164	0.163	0.17	0.191	0.2	RANDOM	25.418

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]
-0.15	-0.08		-0.15		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.003
r_dihedral_angle_4_deg	15.749
r_dihedral_angle_3_deg	12.893
r_dihedral_angle_1_deg	6.187
r_scangle_it	4.212
r_scbond_it	2.796
r_angle_refined_deg	1.318
r_mcangle_it	1.09
r_angle_other_deg	0.976
r_mcbond_it	0.696
r_symmetry_vdw_other	0.269
r_nbd_refined	0.204
r_nbd_other	0.203
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.163
r_symmetry_hbond_refined	0.163
r_mcbond_other	0.161
r_symmetry_vdw_refined	0.101
r_nbtor_other	0.083
r_chiral_restr	0.074
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6976
Nucleic Acid Atoms
Solvent Atoms	771
Heterogen Atoms	191

Software

Software
Software Name	Purpose
CrystalClear	data collection
CCP4	model building
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
CCP4	phasing