6MUJ | pdb_00006muj

Formylglycine generating enzyme bound to copper

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q17

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	296	Crystals were grown by hanging-drop vapor diffusion at 23C for one week using a 2uL:2uL mixture of protein solution (8 mg/ml in 50 mM Tris 7.5, 0.5 M NaCl, 10% glycerol, 1 mM DTT) and precipitant buffer (100 mM Tris 8.0, 3.2 M ammonium formate, 0.3% octyl-beta-glucoside (w/v), 3.2% 2-butanol (v/v)) in Easy-Xtal trays. Crystals were soaked in 1mM DTT (in precipitant buffer) for 15 minutes, then soaked in CuCl2 (in precipitant buffer) for 30 minutes, and finally, backsoaked and cryoprotected in 20% glycerol (in precipitant buffer).

Crystal Properties
Matthews coefficient	Solvent content
3.84	67.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.008	α = 90
b = 140.008	β = 90
c = 217.508	γ = 120

Symmetry
Space Group	P 31 2 1

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	ADSC QUANTUM 315		2015-10-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.115834	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.249	38.738	93.95	12.72	10.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.249	2.33	83.18		0.65	8.8

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2Q17	2.249	38.738	191204	3296	84.41	0.2031	0.2024	0.2023	0.2457	0.2451	48.556

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	8.37
f_angle_d	0.932
f_chiral_restr	0.051
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11247
Nucleic Acid Atoms
Solvent Atoms	653
Heterogen Atoms	84

Software

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