9GNF | pdb_00009gnf

A novel aminotransferase from Streptomyces sp. Gabaculine complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		previous solved unbound protein

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	292.15	0.2 M Potassium thiocynate 0.1 M Bis_tris propane 6.5 20% w/v PEG 3350 1 mM PLP

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.463	α = 90
b = 177.253	β = 90
c = 112.359	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	113.15	PIXEL	DECTRIS EIGER X 16M		2022-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.31	69.59	99.3	1	16.4	5		237241

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.31	1.344	92.3		1		13.3

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.31	69.585	237047	11569	99.303	0.166	0.1646	0.1654	0.185	0.1857	24.223

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]
-0.007			-1.219		1.227

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.228
r_dihedral_angle_3_deg	11.88
r_dihedral_angle_2_deg	7.599
r_lrange_it	6.895
r_dihedral_angle_1_deg	6.305
r_scangle_it	4.488
r_scbond_it	3.159
r_mcangle_it	3.049
r_mcbond_it	2.069
r_angle_refined_deg	2.014
r_nbtor_refined	0.323
r_nbd_refined	0.223
r_symmetry_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.129
r_ncsr_local_group_1	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7090
Nucleic Acid Atoms
Solvent Atoms	1081
Heterogen Atoms	123

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XSCALE	data scaling
MOLREP	phasing