3FDD | pdb_00003fdd

The Crystal Structure of the Pseudomonas dacunhae Aspartate-Beta-Decarboxylase Reveals a Novel Oligomeric Assembly for a Pyridoxal-5-Phosphate Dependent Enzyme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	298	ABDC crystals were grown at 23.5 C using the microbatch under-oil method by mixing in a 1:1 ratio, a 10.5 mg mL-1 ABDC solution in 50 mM Na-Acetate (pH 6.0) and 0.1 mM PLP with a solution containing 100 mM MgCl2, 100 mM Tris (pH 8.5), 25% (v/v) PEG 400, 10% (v/v) glycerol, temperature 298K, pH 7

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.35

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.453	α = 90
b = 150.453	β = 90
c = 150.453	γ = 90

Symmetry
Space Group	I 2 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			2007-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.35	106.6	100	0.076		10.6		22531			39.99

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	2.35	2.41	99.2		0.057		7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	2.35	106.6	22531	1217	99.9	0.17	0.168	0.17	0.212	0.21	RANDOM	39.99

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.981
r_dihedral_angle_4_deg	14.799
r_dihedral_angle_3_deg	13.544
r_dihedral_angle_1_deg	5.301
r_scangle_it	4.08
r_scbond_it	2.715
r_mcangle_it	1.452
r_angle_refined_deg	1.102
r_mcbond_it	0.698
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.187
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.124
r_chiral_restr	0.076
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
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	3948
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	20

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling