3EG4 | pdb_00003eg4

Crystal structure of 2,3,4,5-Tetrahydropyridine-2-carboxylate N-Succinyltransferase from Brucella melitensis biovar abortus 2308

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BXY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	HAMPTON INDEX B11: 2.1M DL MALIC ACID, PH 7.0, VAPOR DIFFUSION, TEMPERATURE 298K, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.808	α = 90
b = 67.808	β = 90
c = 154.83	γ = 120

Symmetry
Space Group	H 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	ADSC QUANTUM 210		2008-06-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.9774	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.87	25.8	98.6	0.097	0.097	12.2	3.3	21653	21653			14.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.87	1.97	91.3		0.442	0.442	2	2.2	2915

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MR, MR	THROUGHOUT	3BXY	1.87	25.8	21642	21642	1113	98.6	0.132	0.132	0.13	0.14	0.166	RANDOM	14.32

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]
0.83			0.83		-1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.168
r_dihedral_angle_3_deg	14.841
r_dihedral_angle_4_deg	10.226
r_dihedral_angle_1_deg	7.096
r_scangle_it	4.191
r_scbond_it	2.735
r_angle_refined_deg	1.683
r_mcangle_it	1.573
r_angle_other_deg	1.015
r_mcbond_it	0.954
r_mcbond_other	0.29
r_chiral_restr	0.105
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2114
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling