6M8T | pdb_00006m8t

Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, FMN complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EJB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	0.05 M Tris pH 8.5, 5 mM magnesium chloride, 50 mM potassium chloride, 5 mM ammonium sulfate, 30% (w/v) PEG400 cryoprotectant 5% PEG200

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.56	α = 90
b = 98.56	β = 90
c = 98.56	γ = 90

Symmetry
Space Group	I 2 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2017-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.67	40.24	100	0.061	0.024	1	22.4	7.4		18632

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.67	1.71	100		1.38	0.55	0.563	1.4	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	2EJB	1.67	40.237	1.34	18620	976	99.88	0.1494	0.1481	0.15	0.1736	0.17	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	21.544
f_angle_d	1.02
f_chiral_restr	0.073
f_bond_d	0.01
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1467
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms	36

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building