2Q17

Formylglycine Generating Enzyme from Streptomyces coelicolor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Y1E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8		100 mM Tris, 2.4 M ammonium formate, 0.3% -octylglucoside, 3.2% 2-butanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.444	α = 90
b = 142.444	β = 90
c = 217.067	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2		ALS	8.2.2

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	2.1	20					123276

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	2.1	2.17

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1Y1E	2.1	20	117425	6203	83.35	0.20106	0.19895	0.24114	RANDOM	41.231

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]
2.37	1.19		2.37		-3.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.921
r_dihedral_angle_4_deg	20.617
r_dihedral_angle_3_deg	13.894
r_dihedral_angle_1_deg	5.905
r_sphericity_free	2.348
r_scangle_it	1.163
r_angle_refined_deg	1.099
r_scbond_it	0.797
r_sphericity_bonded	0.571
r_rigid_bond_restr	0.518
r_mcangle_it	0.422
r_nbtor_refined	0.301
r_mcbond_it	0.283
r_symmetry_hbond_refined	0.216
r_nbd_refined	0.186
r_xyhbond_nbd_refined	0.153
r_symmetry_vdw_refined	0.124
r_metal_ion_refined	0.119
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11130
Nucleic Acid Atoms
Solvent Atoms	976
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement