3D2Y

Complex of the N-acetylmuramyl-L-alanine amidase AmiD from E.coli with the substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4	293	1M LiCl, 10 % PEG 6K, 0.1M ZnCl2, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.274	α = 90
b = 88.274	β = 90
c = 181.834	γ = 120

Symmetry
Space Group	P 61 2 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		2007-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.978850	ESRF	BM30A

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	1.75	47.5	98.6	0.079	28.6	17		42426

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	1.75	1.84	92.7		0.825	2.2	7.1	5643

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	PDB ENTRY 2BGX	1.75	44.15	40210	2136	98.38	0.20919	0.2069	0.25326	RANDOM	12.923

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]
-0.26	-0.13		-0.26		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.9
r_dihedral_angle_3_deg	16.669
r_dihedral_angle_4_deg	15.663
r_dihedral_angle_1_deg	6.582
r_scangle_it	3.924
r_mcangle_it	3.197
r_scbond_it	2.799
r_mcbond_it	2.509
r_angle_refined_deg	1.494
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.9
r_dihedral_angle_3_deg	16.669
r_dihedral_angle_4_deg	15.663
r_dihedral_angle_1_deg	6.582
r_scangle_it	3.924
r_mcangle_it	3.197
r_scbond_it	2.799
r_mcbond_it	2.509
r_angle_refined_deg	1.494
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.186
r_symmetry_hbond_refined	0.117
r_chiral_restr	0.111
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2098
Nucleic Acid Atoms
Solvent Atoms	308
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

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.