2PLJ | pdb_00002plj

Crystal structure of lysine/ornithine decarboxylase complexed with putrescine 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	35% 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
2.21	44.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.074	α = 90
b = 88.683	β = 90
c = 111.843	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	1.7	50	99.9	0.074	0.074	35.9	7		90404	1.4	2	25.4

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	1.7	1.73	100		0.633	0.633	2.46	6.6	4440

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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	1.7	19.72	2	1.4	85679	85679	4528	99.82	0.1824	0.18077	0.1779	0.21311	0.2109	RANDOM	20.866

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]
-0.04			0.01		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.548
r_dihedral_angle_4_deg	12.817
r_dihedral_angle_3_deg	12.587
r_dihedral_angle_1_deg	5.936
r_scangle_it	3.386
r_scbond_it	2.186
r_angle_refined_deg	1.419
r_mcangle_it	1.33
r_mcbond_it	0.849
r_nbtor_refined	0.305
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.208
r_symmetry_vdw_refined	0.179
r_chiral_restr	0.129
r_symmetry_hbond_refined	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5711
Nucleic Acid Atoms
Solvent Atoms	614
Heterogen Atoms	43

Software

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