3I12 | pdb_00003i12

The crystal structure of the D-alanyl-alanine synthetase A from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.1M HEPES, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.153	α = 90
b = 85.813	β = 90
c = 230.893	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	ADSC QUANTUM 315r	mirrors	2008-12-02	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794, 0.9796	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	2.2	115.47	99.87	0.088	29.56	9.8	82180	82073	2	2

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	2.259	98.76		0.799	2.34	9	6236

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.2	47.54	82180	82073	4332	99.87	0.1996	0.19697	0.2	0.24918	0.25	RANDOM	28.034

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]
-0.82			-0.16		0.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.509
r_dihedral_angle_4_deg	23.242
r_dihedral_angle_3_deg	18.166
r_dihedral_angle_1_deg	7.25
r_scangle_it	4.911
r_scbond_it	3.101
r_angle_refined_deg	1.976
r_mcangle_it	1.927
r_angle_other_deg	1.097
r_mcbond_it	1.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.509
r_dihedral_angle_4_deg	23.242
r_dihedral_angle_3_deg	18.166
r_dihedral_angle_1_deg	7.25
r_scangle_it	4.911
r_scbond_it	3.101
r_angle_refined_deg	1.976
r_mcangle_it	1.927
r_angle_other_deg	1.097
r_mcbond_it	1.052
r_mcbond_other	0.247
r_chiral_restr	0.128
r_bond_refined_d	0.022
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	10681
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	108

Software

Software
Software Name	Purpose
SBC-Collect	data collection
HKL-3000	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.