7B4J | pdb_00007b4j

Thermostable omega transaminase PjTA-R6 variant W58M/F86L/R417L engineered for asymmetric synthesis of enantiopure bulky amines

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	293	Drop were prepared by mixing 1ul of protein solution (~10 mg/ml in 20 mM HEPES pH 7.5, 100 mM NaCl, and 20 uM PLP buffer ) with 1ul of reservoir solution. The reservoir contained 0.7-1M Succinic acid pH 7.6. Crystals formed after 48h.

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.822	α = 90
b = 97.822	β = 90
c = 118.716	γ = 90

Symmetry
Space Group	P 43

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 EIGER2 XE 16M		2019-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	50.8	100	0.054	0.06	0.027	0.999	15.1	4.9		87797

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		0.737	0.826	0.368	0.7		4.9

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	1.9	50.8	83494	4254	99.99	0.1792	0.1778	0.2076	RANDOM	33.469

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]
0.07			0.07		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.799
r_dihedral_angle_4_deg	14.957
r_dihedral_angle_3_deg	12.902
r_dihedral_angle_1_deg	6.899
r_angle_refined_deg	1.458
r_angle_other_deg	1.399
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.799
r_dihedral_angle_4_deg	14.957
r_dihedral_angle_3_deg	12.902
r_dihedral_angle_1_deg	6.899
r_angle_refined_deg	1.458
r_angle_other_deg	1.399
r_chiral_restr	0.075
r_bond_refined_d	0.008
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	6901
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	40

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DIALS	data processing
Coot	model building
REFMAC	phasing
xia2	data processing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.