3DFH

crystal structure of putative mandelate racemase / muconate lactonizing enzyme from Vibrionales bacterium SWAT-3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	294	0.1 M MES, 35% MPD, 0.2 M lithium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.836	α = 90
b = 121.836	β = 90
c = 319.347	γ = 90

Symmetry
Space Group	I 4 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		2008-05-29		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9798	Diamond	I04

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	2.2	50	100	0.092	8.5	7.9		116723

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	2.2	2.28	100		0.625		7.8	11652

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	2.2	41.59	61155	3113	100	0.176	0.173	0.234	RANDOM	25.051

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]
					-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.056
r_dihedral_angle_4_deg	23.413
r_dihedral_angle_3_deg	16.023
r_scbond_it	9.341
r_dihedral_angle_1_deg	6.484
r_mcangle_it	4.12
r_angle_refined_deg	1.676
r_scangle_it	1.516
r_mcbond_it	1.213
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.056
r_dihedral_angle_4_deg	23.413
r_dihedral_angle_3_deg	16.023
r_scbond_it	9.341
r_dihedral_angle_1_deg	6.484
r_mcangle_it	4.12
r_angle_refined_deg	1.676
r_scangle_it	1.516
r_mcbond_it	1.213
r_chiral_restr	0.109
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8571
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	3

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHELXD	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.