7EIH | pdb_00007eih

Ancestral L-Lys oxidase (ligand free form)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	12.5% (w/v) PEG3350, 0.1 M HEPES-NaOH (pH 7.5) and 0.2 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.441	α = 90
b = 80.462	β = 90
c = 173.8	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS3 6M		2020-03-25	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	2.2	49.3	98.8	0.106	0.999	18.9	13.5		63996

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	2.2	2.31			0.846	0.868

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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	2.2	49.3	63926	3243	98.607	0.216	0.2136	0.22	0.2552	0.26	38.326

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]
1.256			-1.054		-0.202

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.213
r_dihedral_angle_4_deg	19.984
r_dihedral_angle_3_deg	16.039
r_dihedral_angle_1_deg	7.463
r_lrange_it	7.204
r_lrange_other	7.199
r_scangle_it	5.052
r_scangle_other	5.046
r_mcangle_it	4.651
r_mcangle_other	4.651
r_scbond_it	3.219
r_scbond_other	3.215
r_mcbond_it	3.102
r_mcbond_other	3.101
r_angle_refined_deg	1.498
r_angle_other_deg	1.275
r_symmetry_nbd_refined	0.311
r_nbd_other	0.268
r_nbd_refined	0.198
r_symmetry_nbd_other	0.182
r_xyhbond_nbd_refined	0.176
r_nbtor_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.155
r_chiral_restr	0.075
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_other	0.049
r_ncsr_local_group_1	0.036
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	9529
Nucleic Acid Atoms
Solvent Atoms	498
Heterogen Atoms	116

Software

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