1Z70 | pdb_00001z70

1.15A resolution structure of the formylglycine generating enzyme FGE

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.295	α = 90
b = 109.765	β = 90
c = 43.511	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MARRESEARCH		2004-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.918	BESSY	14.2

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	1.15	41.2	88.2	0.061	23.9			93768

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	1.15	1.17	80.8		0.129	5.4	1.4	4230

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1Y1E	1.15	41.2	89044	4525	87.76	0.13914	0.13759	0.14	0.16991	0.17	RANDOM	12.545

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]
-0.01			0.04		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.719
r_dihedral_angle_4_deg	16.021
r_dihedral_angle_3_deg	13.511
r_sphericity_free	9.773
r_dihedral_angle_1_deg	6.782
r_sphericity_bonded	5.451
r_scangle_it	5.189
r_scbond_it	3.757
r_mcangle_it	3.178
r_mcbond_it	2.291
r_angle_refined_deg	1.769
r_angle_other_deg	1.697
r_rigid_bond_restr	1.552
r_mcbond_other	1.03
r_symmetry_hbond_refined	0.251
r_symmetry_vdw_other	0.238
r_nbd_refined	0.213
r_nbd_other	0.212
r_symmetry_vdw_refined	0.205
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.104
r_nbtor_other	0.089
r_metal_ion_refined	0.069
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2192
Nucleic Acid Atoms
Solvent Atoms	546
Heterogen Atoms	45

Software

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