2PLK | pdb_00002plk

Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F3T	PDB ENTRY 1F3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.4	277	30% PEG-4000, 0.1M Tris HCl pH8.4, 0.2M Magnesium chloride, 0.5% w/v n-octyl-b-D-glucoside , VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.1	41.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.245	α = 90
b = 88.027	β = 90
c = 99.272	γ = 90

Symmetry
Space Group	P 21 21 21

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	SBC-3		2006-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.979269	APS	19-BM

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	2.14	50	90.6	0.107	0.107	14.6	4.4		37184	1.4	2

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	2.14	2.19	87.7		0.429	0.429	2	2.7

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	PDB ENTRY 1F3T	2.14	24.81	35254	35254	1882	89.91	0.17791	0.17451	0.19	0.24003	0.25	RANDOM	26.185

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]
2.51			0.08		-2.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.089
r_dihedral_angle_4_deg	17.6
r_dihedral_angle_3_deg	16.005
r_dihedral_angle_1_deg	6.451
r_scangle_it	2.99
r_scbond_it	1.886
r_angle_refined_deg	1.517
r_mcangle_it	1.171
r_mcbond_it	0.699
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.285
r_nbd_refined	0.208
r_symmetry_vdw_refined	0.186
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.095
r_bond_refined_d	0.014
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_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	5666
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	44

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing