8G8P | pdb_00008g8p

F420-2/GTP(GDP) complex of F420-gamma glutamyl ligase (CofE) from Archaeoglobus fulgidus

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ULE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	291	0.8 M ammonium sulfate, 0.1 M citrate pH 4.5, 2 mM GTP, 5 mM Mn2+, 1 mM F420-2

Crystal Properties
Matthews coefficient	Solvent content
1.95	36.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.238	α = 90
b = 68.238	β = 90
c = 91.807	γ = 90

Symmetry
Space Group	P 41 2 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	DECTRIS EIGER X 16M		2018-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95372	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.83	48.3	100	0.039	0.998	13.7	13.7		19796

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.88	100		0.333	0.599

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	1.83	48.298	19775	940	99.843	0.198	0.197	0.2	0.2191	0.23	28.422

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]
-0.031			-0.031		0.061

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.252
r_dihedral_angle_4_deg	15.471
r_dihedral_angle_3_deg	12.709
r_dihedral_angle_1_deg	6.776
r_lrange_it	3.201
r_lrange_other	3.155
r_scangle_other	1.926
r_scangle_it	1.917
r_mcangle_it	1.655
r_mcangle_other	1.654
r_scbond_it	1.301
r_angle_refined_deg	1.276
r_scbond_other	1.226
r_angle_other_deg	1.167
r_mcbond_it	1.059
r_mcbond_other	1.054
r_symmetry_nbd_refined	0.191
r_nbd_other	0.186
r_nbd_refined	0.179
r_symmetry_nbd_other	0.167
r_nbtor_refined	0.145
r_xyhbond_nbd_refined	0.125
r_symmetry_xyhbond_nbd_refined	0.091
r_symmetry_nbtor_other	0.07
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1849
Nucleic Acid Atoms
Solvent Atoms	126
Heterogen Atoms	122

Software

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