9J0V

Crystal structure of monomeric PLP-dependent transaminase from Desulfobacula toluolica in P 21 21 21 space group

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		288	0.1M Ammonium acetate, 0.1M Bis-tris pH 5.5, 17% PEG 10000

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.847	α = 90
b = 56.226	β = 90
c = 118.625	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 EIGER X 16M		2021-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.88560	ESRF	ID23-1

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	1.79	40.81	98.8	0.047	0.056	0.028	0.998	13.4	3.6		24352

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	1.79	1.83		96.2	0.67	0.787	0.405	0.686		3.4

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	1.79	40.81	23150	1146	98.51	0.19522	0.19325	0.23575	RANDOM	38.029

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]
-0.15			-0.8		0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.653
r_dihedral_angle_4_deg	18.155
r_dihedral_angle_3_deg	15.413
r_long_range_B_other	9.677
r_long_range_B_refined	9.664
r_scangle_other	7.953
r_dihedral_angle_1_deg	7.366
r_mcangle_it	6.148
r_mcangle_other	6.146
r_scbond_it	5.892
r_scbond_other	5.889
r_mcbond_other	4.779
r_mcbond_it	4.776
r_angle_refined_deg	2.1
r_angle_other_deg	1.501
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_gen_planes_other	0.004
r_bond_other_d	0.003
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	1872
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction