3N75 | pdb_00003n75

X-ray Crystal Structure of the Escherichia coli Inducible Lysine Decarboxylase LdcI

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	285	18-28% (v/v) PEG1000, 0.1 M Sodium Chloride, 0.1 M Tris HCl pH 8.5, 0.005 M Tris[2-carboxyethyl] phosphine, 15% (v/v) glycerol. Once crystals formed, they were soaked in mother liquid that had been saturated with hexatantalum dodecabromide for derivatization., VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 271.76	α = 90
b = 181.993	β = 125.41
c = 170.902	γ = 90

Symmetry
Space Group	C 1 2 1

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		2006-03-22	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2006-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.254431	APS	19-BM
2	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9002	APS	14-BM-C

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
1,2	2	140.3	99.8	0.161	12.6	5.44	454474	454474

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	2	2.1	99.3		0.3266	3.82	3.39	61407

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 1ORD	2	49.89	454474	430750	22770	99.76	0.16886	0.16753	0.17	0.19392	0.19	RANDOM	27.734

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]
0.43		-0.84	0.32		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.012
r_dihedral_angle_4_deg	15.212
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_1_deg	12.177
r_scangle_it	4.244
r_scbond_it	2.865
r_angle_refined_deg	1.633
r_mcangle_it	1.562
r_mcbond_it	1.364
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.012
r_dihedral_angle_4_deg	15.212
r_dihedral_angle_3_deg	12.802
r_dihedral_angle_1_deg	12.177
r_scangle_it	4.244
r_scbond_it	2.865
r_angle_refined_deg	1.633
r_mcangle_it	1.562
r_mcbond_it	1.364
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.219
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.148
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.113
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	28485
Nucleic Acid Atoms
Solvent Atoms	3292
Heterogen Atoms	293

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.