28YL | pdb_000028yl

Crystal structure of the zeamine pathway ketoreductase Zmn13-KR, in complex with NADH

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	7.2	293	0.1 M HEPES, 10% (v/v) isopropanol, 5% (v/v) glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.342	α = 90
b = 109.321	β = 90
c = 208.278	γ = 90

Symmetry
Space Group	C 2 2 21

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		2025-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8731	ESRF	ID30B

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	1.9	64.74	97.7	0.103	0.118	0.056	0.996	7.2	3.9		70494			26.1

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	1.9	1.94	95.3		0.577	0.668	0.327	0.748	1.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	64.739	70468	3536	97.266	0.186	0.1844	0.1844	0.2246	0.2246	RANDOM	31.741

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]
-0.009			0.009		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.612
r_dihedral_angle_3_deg	13.542
r_lrange_it	7.405
r_dihedral_angle_2_deg	7.105
r_dihedral_angle_1_deg	6.375
r_scangle_it	5.606
r_scbond_it	3.772
r_mcangle_it	3.74
r_mcbond_it	2.553
r_angle_refined_deg	1.454
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.195
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.103
r_ncsr_local_group_5	0.088
r_ncsr_local_group_6	0.087
r_ncsr_local_group_4	0.083
r_ncsr_local_group_1	0.079
r_ncsr_local_group_3	0.079
r_ncsr_local_group_2	0.077
r_bond_refined_d	0.006
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7203
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	208

Software

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