6OW4

Structure of the NADH-bound form of 20beta-Hydroxysteroid Dehydrogenase from Bifidobacterium adolescentis strain L2-32

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6M9U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		296	Mutant S181A 20beta-HSDH purified recombinant protein was incubated with 2.5 mM NADH and 0.25mM or 0.5 mM cortisol for 2 hours at 4C. Crystals were grown in condition 86 of the Hampton PEG/Ion screen containing 0.05 M Citric acid, 0.05 M BIS-TRIS propane / pH 5.0, and 16% w/v Polyethylene glycol 3,350. The condition was then optimized in hanging-drop format using 18-20% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 165.078	α = 90
b = 134.71	β = 100.15
c = 96.396	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2018-03-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.07	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.99	103.71	54.3	0.995	6.3	4.8		73226			16.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.045

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	6M9U	1.99	103.71	69584	3672	51.96	0.19	0.18744	0.2384	RANDOM	24.515

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]
0.16		0.76	-0.64		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.659
r_dihedral_angle_4_deg	18.333
r_dihedral_angle_3_deg	12.763
r_dihedral_angle_1_deg	5.627
r_long_range_B_refined	2.173
r_long_range_B_other	2.173
r_angle_refined_deg	1.188
r_mcangle_it	1.173
r_mcangle_other	1.173
r_angle_other_deg	1.125
r_scangle_other	1.041
r_mcbond_it	0.776
r_mcbond_other	0.776
r_scbond_it	0.726
r_scbond_other	0.726
r_rigid_bond_restr	0.276
r_chiral_restr	0.036
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16825
Nucleic Acid Atoms
Solvent Atoms	451
Heterogen Atoms	352

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
autoPROC	data scaling
PHENIX	phasing