4E5T | pdb_00004e5t

Crystal structure of a putative Mandelate racemase/Muconate lactonizing enzyme (Target PSI-200750) from Labrenzia alexandrii DFL-11

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	298	Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (20% PEG1000, 0.1M Cacodylate 6.5, 0.2M MgCl2 Wizard II #44); Cryoprotection (Ethylene glycol), Sitting Drop Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.9	α = 90
b = 156.88	β = 90
c = 218.24	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	ADSC QUANTUM 315	MIRRORS	2011-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.0750	NSLS	X29A

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	2.9		100	0.14	18.73			75923		-3	49.935

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	2.9	2.98	100		0.953	2.89

Refinement

Statistics
Diffraction ID	Structure Solution Method	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	2.9	49.45	1.34	75910	3817	99.97	0.1676	0.1635	0.16	0.2422	0.24	56.4834

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]
2.5152			-9.5236		7.0084

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.246
f_angle_d	1.188
f_chiral_restr	0.077
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	23603
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	8

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

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.