3N2T | pdb_00003n2t

Structure of the glycerol dehydrogenase AKR11B4 from Gluconobacter oxydans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	protein stock solution: 10 mg/ml AKR11B4 protein, 10 mM Tris/HCl puffer, 150 mM NaCl, 0.5 mM EDTA, pH 8.5. Reservoir solution: 35 % (w/v) poly ethylen glycol 3350 (PEG 3350), 200 mM potassium nitrate. The crystallization drop contained equal volumes of the reservoir and the protein stock solution before equilibration. The pH-value in the crystallization drop was determined by the buffer of the protein stock solution., VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.25	α = 90
b = 62.39	β = 90.47
c = 59.82	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						M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.9537	EMBL/DESY, HAMBURG	X11

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	2	34.5	99.8	0.133	0.133	10.1	5.4		26999			29.1

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	24.119	1.37	20591	1029	99.86	0.1907	0.1885	0.18	0.2316	0.22

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]
2.2631		3.2464	-5.1194		2.8563

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.788
f_angle_d	0.963
f_chiral_restr	0.067
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2585
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling