8GYJ | pdb_00008gyj

Crystal structure of Fic25 complexed with PLP-(5S,6S)-N2-acetyl-DADH adduct from Streptomyces ficellus

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	1.1 M Sodium citrate, 0.1 M Imidazole, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 201.443	α = 90
b = 201.443	β = 90
c = 57.003	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS3 6M		2022-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.82	48.43	100	0.113	0.999	17.8	10.4		118807

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.85			0.98	0.827

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8GYH	1.82	48.43	112809	5971	99.95	0.1604	0.1591	0.17	0.1851	0.19	RANDOM	22.242

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]
0.47	0.24		0.47		-1.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.089
r_dihedral_angle_4_deg	13.208
r_dihedral_angle_3_deg	12.255
r_dihedral_angle_1_deg	5.953
r_angle_refined_deg	1.229
r_angle_other_deg	1.195
r_chiral_restr	0.05
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6357
Nucleic Acid Atoms
Solvent Atoms	896
Heterogen Atoms	95

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

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.