1Y4J

Crystal structure of the paralogue of the human formylglycine generating enzyme

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	Tris/HCl, MPD, CaCl2, PEG8000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.078	α = 90
b = 100.75	β = 101.68
c = 62.704	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	MARRESEARCH		2004-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (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	1.86	50	98.7	0.055	22.7	3.6		47438			29.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.93	87.3		0.586	1.8	3	4141

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIRAS	THROUGHOUT	1.864	32	45026	2387	99.35	0.17185	0.16996	0.20548	RANDOM	28.299

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]
1.29		1.23	-0.61		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.339
r_dihedral_angle_4_deg	16.948
r_dihedral_angle_3_deg	14.85
r_dihedral_angle_1_deg	6.606
r_scangle_it	2.857
r_scbond_it	1.906
r_mcangle_it	1.413
r_angle_refined_deg	1.338
r_mcbond_it	0.925
r_angle_other_deg	0.811
r_symmetry_vdw_other	0.257
r_nbd_refined	0.203
r_nbd_other	0.202
r_mcbond_other	0.185
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.174
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.142
r_metal_ion_refined	0.091
r_nbtor_other	0.085
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4283
Nucleic Acid Atoms
Solvent Atoms	562
Heterogen Atoms	78

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing