8WK5

Aldo-keto reductase KmAKR-Y28A/K29H/Y296W/W297H

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	Magnesium chloride hexahydrate, TRIS hydrochloride, Polyethylene glycol 4000, glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.616	α = 90
b = 115.979	β = 102.31
c = 83.828	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	100	PIXEL	DECTRIS EIGER X 9M		2022-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.9	115.98	98.3	0.437	0.536	0.307	0.746	3.8	2.9		27573

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.08		99.2	1.988	2.466	1.439	0.159		2.8

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	AlphaFold	2.9	57.86	26203	1343	98.11	0.26983	0.26763	0.31194	RANDOM	34.437

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]
5.42		4.1	-3.07		-3.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.407
r_dihedral_angle_1_deg	6.367
r_long_range_B_refined	5.37
r_long_range_B_other	5.37
r_dihedral_angle_2_deg	4.388
r_scangle_other	2.963
r_mcangle_it	2.871
r_mcangle_other	2.87
r_mcbond_it	1.63
r_mcbond_other	1.63
r_scbond_it	1.624
r_scbond_other	1.624
r_angle_refined_deg	0.924
r_angle_other_deg	0.301
r_chiral_restr	0.043
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9672
Nucleic Acid Atoms
Solvent Atoms	15
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing