8VR5

crystal structure of the Pcryo_0618 aminotransferase from Psychrobacter cryohalolentis K5 in the presence of PMP and glutamate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8VR3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	Protein incubated with 1.0 mM PLP and 5 mM UDP-4-amino-2,3-diacetoamido-2,3,4-trideoxy-L-arabinose. Precipitant: 8-12% PEG 8000, 100 mM magnesium chloride, and 100 mM Homo-PIPES (pH 5)

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.493	α = 90
b = 159.822	β = 90
c = 115.864	γ = 90

Symmetry
Space Group	P 21 21 2

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		2019-08-22	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	2.2	50	99.6	0.078	15.6	8.3		123706

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	2.2	2.3	98.9		0.34	3.2	5.1

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	2.2	32.89	117412	6297	99.65	0.17998	0.17816	0.21348	RANDOM	22.968

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]
-0.01			0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.119
r_dihedral_angle_2_deg	8.745
r_long_range_B_refined	7.247
r_long_range_B_other	7.247
r_dihedral_angle_1_deg	6.723
r_scangle_other	5.689
r_mcangle_it	3.665
r_mcangle_other	3.665
r_scbond_it	3.461
r_scbond_other	3.461
r_mcbond_it	2.311
r_mcbond_other	2.31
r_angle_refined_deg	1.572
r_angle_other_deg	0.508
r_chiral_restr	0.116
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	11583
Nucleic Acid Atoms
Solvent Atoms	857
Heterogen Atoms	185

Software

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