Experiment: 7SIR

Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate ligase from Acinetobacter baumannii AB5075-UW

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A5F	5a5f in three domains as per Morda

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	287	Rigaku Reagens JCSG+ screen, condition A5: 200mM Magnesiumformate, 20% (w/V) PEG 3350: AcbaC.17938.a.B1 at 40mg/ml: tray 321638 a4b: cryo: 20% EG: puck pxu9-10.

Crystal Properties
Matthews coefficient	Solvent content
2.46	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.17	α = 90
b = 86.24	β = 90
c = 94.3	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	RAYONIX MX-300	Beryllium Lenses	2021-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.9787	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	1.65	50	99.2	0.053	0.057	0.999	20.98	7.233		58267			31.511

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69	96.8		0.513	0.559	0.875	3.29	6.279

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	5a5f in three domains as per Morda	1.65	47.15	1.35	58259	2028	99.14	0.1685	0.1677	0.1684	0.1921	0.1927	0	29.84

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.6406
f_angle_d	0.9209
f_chiral_restr	0.0621
f_plane_restr	0.0071
f_bond_d	0.0069

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3196
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	6

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building