3AI3

The crystal structure of L-Sorbose reductase from Gluconobacter frateurii complexed with NADPH and L-sorbose

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3AI2	PDB ENTRY 3AI2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	Crystals of the His116Leu mutant of SR containing 10 mM NADPH and 100 mM L-sorbose were obtained under a reservoir solution condition of 30% (w/v) PEG400, 200 mM calcium chloride and 100 mM sodium acetate trihydrate, pH 4.5. The crystals of SR complexed with NADPH and L-sorbose were prepared by soaking the crystals in the reservoir solution supplemented with 2 M L-sorbose and 10 mM NADPH for 12 h at 293 K., VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.04	α = 90
b = 124.41	β = 90
c = 124.54	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		CCD	ADSC QUANTUM 270		2009-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.000	Photon Factory	AR-NE3A

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	1.8	20	99.8	0.083	21.3			88419	1.0001	1

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	1.8	1.85	100		0.465	5.6

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 3AI2	1.8	19.69	83987	4432	99.84	0.21416	0.2123	0.24941	RANDOM	12.871

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]
0.93			0.51		-1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.165
r_dihedral_angle_4_deg	15.829
r_dihedral_angle_3_deg	13.697
r_dihedral_angle_1_deg	5.584
r_scangle_it	3.831
r_scbond_it	2.358
r_angle_refined_deg	1.476
r_mcangle_it	1.308
r_mcbond_it	0.693
r_chiral_restr	0.099

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.165
r_dihedral_angle_4_deg	15.829
r_dihedral_angle_3_deg	13.697
r_dihedral_angle_1_deg	5.584
r_scangle_it	3.831
r_scbond_it	2.358
r_angle_refined_deg	1.476
r_mcangle_it	1.308
r_mcbond_it	0.693
r_chiral_restr	0.099
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7956
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	300

Software

Software
Software Name	Purpose
ADSC	data collection
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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 R01GM133198.