3LK7

The Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate (MurD) ligase from Streptococcus agalactiae to 1.5A

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	25% PEG 3350, 0.1M Tris pH 8.5, 0.2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 161.539	α = 90
b = 65.045	β = 107.52
c = 52.889	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	ADSC QUANTUM 315		2009-07-07		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	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	1.5	50	99.5	0.084	9.7	3.7		83028

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)
	1.5	1.55	99.4		0.473		3.7	8296

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.5	50	82903	4139	98.94	0.188	0.187	0.208	RANDOM	24.037

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]
-1.72		-0.74	2.27		-1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.79
r_dihedral_angle_3_deg	11.707
r_dihedral_angle_4_deg	11.175
r_dihedral_angle_1_deg	5.965
r_scangle_it	3.846
r_scbond_it	2.477
r_mcangle_it	1.427
r_angle_refined_deg	1.342
r_mcbond_it	0.801
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.79
r_dihedral_angle_3_deg	11.707
r_dihedral_angle_4_deg	11.175
r_dihedral_angle_1_deg	5.965
r_scangle_it	3.846
r_scbond_it	2.477
r_mcangle_it	1.427
r_angle_refined_deg	1.342
r_mcbond_it	0.801
r_chiral_restr	0.09
r_bond_refined_d	0.011
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3438
Nucleic Acid Atoms
Solvent Atoms	401
Heterogen Atoms	11

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

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.