5EP9

Crystal structure of the non-heme alpha ketoglutarate dependent epimerase SnoN from nogalamycin biosynthesis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OPW	ensemble of 2opw, 2a1x, 2fct
experimental model	PDB	2A1X	ensemble of 2opw, 2a1x, 2fct
experimental model	PDB	2FCT	ensemble of 2opw, 2a1x, 2fct

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	PEG3350, ammonium acetate, Bis-Tris, ammonium ferric citrate, alpha ketoglutarate, sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.207	α = 90
b = 120.557	β = 92.54
c = 102.879	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 PILATUS 6M		2015-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9724	ESRF	ID29

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	2.07	47.8	99.5	0.077	11.7	4.9	379883	76968			37.7

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	2.07	2.13	99.5		0.995	1.4

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	ensemble of 2opw, 2a1x, 2fct	2.13	47.8	67031	3557	99.37	0.17725	0.17585	0.20312	RANDOM	48.491

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]
-1.1		-0.46	2.28		-1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.037
r_dihedral_angle_4_deg	20.839
r_dihedral_angle_3_deg	13.484
r_long_range_B_refined	7.677
r_long_range_B_other	7.63
r_dihedral_angle_1_deg	7.213
r_scangle_other	4.084
r_mcangle_other	3.211
r_mcangle_it	3.21
r_scbond_it	2.519
r_scbond_other	2.519
r_mcbond_it	2.012
r_mcbond_other	2.002
r_angle_other_deg	1.961
r_angle_refined_deg	1.959
r_chiral_restr	0.11
r_bond_refined_d	0.021
r_gen_planes_refined	0.014
r_bond_other_d	0.012
r_gen_planes_other	0.01
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	7565
Nucleic Acid Atoms
Solvent Atoms	457
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing