3N2B | pdb_00003n2b

1.8 Angstrom Resolution Crystal Structure of Diaminopimelate Decarboxylase (lysA) from Vibrio cholerae.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P3E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	Protein solution: 7.8 mg/mL, 0.25M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (D8) 0.2M Ammonium chloride, 0.1M Tris pH 8.0, 20%(w/v) PEG6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.394	α = 105.31
b = 80.329	β = 93.62
c = 118.693	γ = 90.52

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	Beryllium lenses	2010-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.8	30	97.5	0.048	17.4	2.6	147832	147832		-3	28.3

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)
	1.8	1.83	96.2		0.363	2.7	2.6	7354

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	2P3E	1.8	29.94	138491	138491	7289	97.51	0.18449	0.18449	0.18266	0.19	0.21874	0.22	RANDOM	31.855

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]
1.51	0.34	-0.25	-2.98	-1.49	0.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.451
r_dihedral_angle_4_deg	13.373
r_dihedral_angle_3_deg	9.495
r_scangle_it	4.63
r_dihedral_angle_1_deg	3.243
r_scbond_it	2.928
r_mcangle_it	2.072
r_angle_refined_deg	1.392
r_mcbond_it	1.214
r_angle_other_deg	0.846

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.451
r_dihedral_angle_4_deg	13.373
r_dihedral_angle_3_deg	9.495
r_scangle_it	4.63
r_dihedral_angle_1_deg	3.243
r_scbond_it	2.928
r_mcangle_it	2.072
r_angle_refined_deg	1.392
r_mcbond_it	1.214
r_angle_other_deg	0.846
r_mcbond_other	0.327
r_chiral_restr	0.089
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12599
Nucleic Acid Atoms
Solvent Atoms	1121
Heterogen Atoms	4

Software

Software
Software Name	Purpose
Blu-Ice	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.