8JM2

Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (Form B)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LR8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.25	291	tris-bicine, 100 mM, pH 8.25; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 24%, v/v; PEG 20000, 12%, w/v

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.558	α = 90
b = 91.312	β = 90
c = 130.692	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		2018-04-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97918	SSRF	BL19U1

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	50	95.3	0.075	0.083	0.037	0.992	14.3	4.8		45525

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	1.93	74.2		0.393	0.483	0.272	0.834		2.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.9	33.6	42871	2306	94.59	0.16192	0.15999	0.19712	RANDOM	19.864

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]
0.67			-0.22		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.122
r_dihedral_angle_4_deg	17.004
r_dihedral_angle_3_deg	12.346
r_dihedral_angle_1_deg	7.625
r_long_range_B_refined	5.216
r_long_range_B_other	5.092
r_scangle_other	4.056
r_scbond_it	2.702
r_scbond_other	2.701
r_mcangle_other	2.553
r_mcangle_it	2.552
r_mcbond_it	1.792
r_mcbond_other	1.785
r_angle_refined_deg	1.771
r_angle_other_deg	1.436
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001
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	3928
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	197

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-3000	data reduction
PHASER	phasing