7L7X

X-ray structure of the Pcryo_0638 aminotransferase from Psychrobacter cryohalolentis

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	18-22% PEG-8000, 200 mM tetramethylammonium chloride. protein incubated with 1 mM PLP and 5 mM UDP-2-acetamido-4-amino-2,4,6-trideoxy-D-glucose

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.529	α = 81.747
b = 63.141	β = 78.593
c = 69.853	γ = 66.818

Symmetry
Space Group	P 1

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	Bruker PHOTON II		2018-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	BRUKER D8 QUEST	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	1.3	50	92.9	0.057	7.2	2.4		202026

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.4	83		0.229	1.9	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3frk	1.3	29.957	202026	10084	92.941	0.151	0.1499	0.1692	12.793

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]
0.478	-0.142	0.052	-0.374	-0.116	-0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.387
r_dihedral_angle_4_deg	15.917
r_dihedral_angle_3_deg	12.467
r_dihedral_angle_1_deg	7.083
r_lrange_it	5.451
r_lrange_other	5.451
r_scangle_it	3.052
r_scangle_other	3.051
r_scbond_it	2.021
r_scbond_other	2.021
r_mcangle_it	1.862
r_mcangle_other	1.862
r_angle_other_deg	1.496
r_angle_refined_deg	1.472
r_mcbond_it	1.194
r_mcbond_other	1.192
r_xyhbond_nbd_refined	0.232
r_nbd_refined	0.227
r_symmetry_xyhbond_nbd_refined	0.219
r_nbd_other	0.208
r_symmetry_xyhbond_nbd_other	0.198
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.174
r_symmetry_nbd_refined	0.157
r_metal_ion_refined	0.139
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6166
Nucleic Acid Atoms
Solvent Atoms	1280
Heterogen Atoms	190

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing