3LGX | pdb_00003lgx

Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3L8C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	298	0.1 M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.41	α = 90
b = 174.41	β = 90
c = 176.065	γ = 90

Symmetry
Space Group	P 41 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		2009-11-05		SINGLE WAVELENGTH
2	1		CCD	ADSC QUANTUM 315		2009-11-20

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9793	APS	24-ID-E
2	SYNCHROTRON	NSLS BEAMLINE X29A	0.9793	NSLS	X29A

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	2.6	50	99.7	0.102	7.1	4.2		149144

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)
	2.65	2.7	100		0.826		4.2	7463

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	3L8C	2.6	50	83022	4149	99.69	0.221	0.218	0.21	0.276	0.27	RANDOM	50.971

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]
0.52			0.52		-1.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.919
r_dihedral_angle_4_deg	22.136
r_dihedral_angle_3_deg	19.835
r_dihedral_angle_1_deg	6.395
r_scangle_it	3.698
r_scbond_it	2.161
r_mcangle_it	1.62
r_angle_refined_deg	1.582
r_mcbond_it	0.848
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.919
r_dihedral_angle_4_deg	22.136
r_dihedral_angle_3_deg	19.835
r_dihedral_angle_1_deg	6.395
r_scangle_it	3.698
r_scbond_it	2.161
r_mcangle_it	1.62
r_angle_refined_deg	1.582
r_mcbond_it	0.848
r_chiral_restr	0.108
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15888
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	124

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

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.