3R1Z | pdb_00003r1z

Crystal structure of NYSGRC enolase target 200555, a putative dipeptide epimerase from Francisella philomiragia : Complex with L-Ala-L-Glu and L-Ala-D-Glu

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapour diffusion, sitting drop	5.6	294	Protein: 10 mM HEPES pH 7.5, 150 mM Nacl, 10% glycerol, 5 mM DTT; Reservoir: 2M Ammonium Sulfate, 100 mM NaCitrate, 200 mM KNaTartrate; Soak: 2.2 M Ammonium sulfate, 100 mM MES pH 6.0, 18% glycerol, 50mM MgSO4, 25 mM L-Ala-L-Glu, 30 min, vapour diffusion, sitting drop, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.19	α = 90
b = 121.19	β = 90
c = 149.02	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	CCD	RAYONIX MX225HE	Undulator Source			SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97905	APS	31-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.9	50	97.9	0.097	0.097	16.4	12.5	85703	85703			19.31

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	92.5		0.38	0.38	5.8	12.1	3006

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	FOURIER SYNTHESIS	1.9	29.69	84359	84359	4221	96.28	0.1585	0.1585	0.1571	0.157	0.1854	0.1841	Random	24.6422

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]
0.258			0.258		0.7469

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.337
f_angle_d	1.242
f_chiral_restr	0.1
f_bond_d	0.008
f_plane_restr	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5605
Nucleic Acid Atoms
Solvent Atoms	708
Heterogen Atoms	84

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
SCALEPACK	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.