8JM3

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

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
2.5	50.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.648	α = 90
b = 91.713	β = 90
c = 129.724	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		2018-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.97891	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	99.9	0.114	0.12	0.036	0.998	5	10.9		47153

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	100		0.839	0.879	0.261	0.86		11.2

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	39.46	44669	2421	99.52	0.16085	0.15902	0.19474	RANDOM	29.149

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]
-0.18			-0.95		1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.704
r_dihedral_angle_4_deg	16.081
r_dihedral_angle_3_deg	12.446
r_dihedral_angle_1_deg	7.501
r_long_range_B_other	6.177
r_long_range_B_refined	6.17
r_scangle_other	5.047
r_scbond_it	3.484
r_scbond_other	3.479
r_mcangle_it	3.247
r_mcangle_other	3.246
r_mcbond_it	2.525
r_mcbond_other	2.521
r_angle_refined_deg	1.717
r_angle_other_deg	1.422
r_chiral_restr	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
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	3948
Nucleic Acid Atoms
Solvent Atoms	296
Heterogen Atoms	161

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing