4MUQ

Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F78	pdb entry 4F78

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.3	273	0.2 M ammonium sulfate, 0.1 M sodium cacodylate and 30% polyethylene glycol (PEG) 8K, 75 mM PHY D-Ala-D-Ala phosphinate analog, VAPOR DIFFUSION, SITTING DROP, temperature 273K, pH 6.3

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.895	α = 90
b = 43.728	β = 99.2
c = 80.236	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MAR scanner 300 mm plate		2013-07-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.27689	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	1.36	79.2	96.9	0.063	17.2	7.7		54882		-2

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	1.36	1.47	94.2		0.578	3	7.6	10918

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	THROUGHOUT	pdb entry 4F78	1.364	38.395	1.34	54882	2678	96.53	0.1631	0.1619	0.16	0.1846	0.18	random

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	14.795
f_angle_d	1.397
f_chiral_restr	0.085
f_bond_d	0.014
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2054
Nucleic Acid Atoms
Solvent Atoms	285
Heterogen Atoms	72

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	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.