5D00

Crystal structure of BshA from B. subtilis complexed with N-acetylglucosaminyl-malate and UMP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	2% (v/v) tascimate, 6% (w/v) PEG-3400, 25 mM NaCl, 10 mM HEPES, 5 mM UDP-N-acetylglucosamine

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.66	α = 90
b = 164.627	β = 90
c = 97.729	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 300 mm CCD		2014-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.078	APS	21-ID-D

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	2.15	93.73	100	0.093	15	9.6		40122

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	2.15	2.27	100		0.69	3.7	9.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3MBO	2.15	82.31	38084	2010	99.96	0.1868	0.1843	0.2341	RANDOM	41.659

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]
-0.15			-0.26		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.569
r_dihedral_angle_4_deg	18.877
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_1_deg	6.809
r_mcangle_it	4.972
r_mcbond_it	3.475
r_mcbond_other	3.462
r_angle_refined_deg	1.823
r_angle_other_deg	0.841
r_chiral_restr	0.102

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.569
r_dihedral_angle_4_deg	18.877
r_dihedral_angle_3_deg	15.324
r_dihedral_angle_1_deg	6.809
r_mcangle_it	4.972
r_mcbond_it	3.475
r_mcbond_other	3.462
r_angle_refined_deg	1.823
r_angle_other_deg	0.841
r_chiral_restr	0.102
r_bond_refined_d	0.017
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	5555
Nucleic Acid Atoms
Solvent Atoms	89
Heterogen Atoms	72

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALA	data scaling
XDS	data scaling
Coot	model building

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.