3N29 | pdb_00003n29

Crystal structure of carboxynorspermidine decarboxylase complexed with Norspermidine from Campylobacter jejuni

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	2.75 M AmSO4, 0.1 M BICINE pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.498	α = 90
b = 144.498	β = 90
c = 79.901	γ = 90

Symmetry
Space Group	P 43 21 2

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 315		2009-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97948	APS	19-ID

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	1.9	102.06	99.8	0.136			66838	66670	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.95	98.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	SAD	THROUGHOUT	1.9	102.06	2	66838	66670	3376	99.75	0.179	0.18145	0.179	0.2017	0.21858	0.2381	RANDOM	14.582

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]
-0.47			-0.47		0.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.998
r_dihedral_angle_3_deg	14.395
r_dihedral_angle_4_deg	12.702
r_dihedral_angle_1_deg	6.781
r_scangle_it	4.498
r_scbond_it	3.091
r_mcangle_it	1.886
r_angle_refined_deg	1.824
r_mcbond_it	1.132
r_angle_other_deg	0.988

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.998
r_dihedral_angle_3_deg	14.395
r_dihedral_angle_4_deg	12.702
r_dihedral_angle_1_deg	6.781
r_scangle_it	4.498
r_scbond_it	3.091
r_mcangle_it	1.886
r_angle_refined_deg	1.824
r_mcbond_it	1.132
r_angle_other_deg	0.988
r_mcbond_other	0.418
r_chiral_restr	0.122
r_bond_refined_d	0.024
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5873
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	51

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.