7EII

Ancestral L-Lys oxidase K387A variant (L-Lys binding form)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	25%(w/v) PEG3350, 0.1 M Tris-HCl (pH 8.5)

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.829	α = 90
b = 80.086	β = 90.425
c = 87.986	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 PILATUS3 6M		2020-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	42.9	99.8	0.087	0.998	16.2	6.8		46762

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53			0.421	0.926

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7EIH	2.4	42.9	46749	2378	99.806	0.185	0.1828	0.2308	35.543

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]
0.645		1.747	-1.198		0.528

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.124
r_dihedral_angle_4_deg	21.265
r_dihedral_angle_3_deg	15.839
r_dihedral_angle_1_deg	7.721
r_lrange_it	7.286
r_lrange_other	7.284
r_scangle_it	4.709
r_scangle_other	4.709
r_mcangle_it	4.301
r_mcangle_other	4.301
r_scbond_it	2.953
r_scbond_other	2.953
r_mcbond_it	2.778
r_mcbond_other	2.778
r_angle_refined_deg	1.46
r_angle_other_deg	1.282
r_nbd_other	0.221
r_nbd_refined	0.207
r_symmetry_xyhbond_nbd_refined	0.194
r_symmetry_nbd_other	0.187
r_xyhbond_nbd_refined	0.187
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.156
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9495
Nucleic Acid Atoms
Solvent Atoms	369
Heterogen Atoms	116

Software

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