2F3O | pdb_00002f3o

Crystal Structure of a glycyl radical enzyme from Archaeoglobus fulgidus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R9D	pdb entry 1R9D

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	16 % PEG8000, 8 % isopropanol, 80 mM Hepes pH 7.5, 160 mM ammonium sulphate, 1 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 167.03	α = 90
b = 174.17	β = 90
c = 162.46	γ = 90

Symmetry
Space Group	C 2 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	CCD	ADSC QUANTUM 4		2004-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.00	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.9	20	98.6	0.087	20.61		52531	52531		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3	97.2		0.449	5.34		36376

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1R9D	2.9	19.69	52529	52529	2648	100	0.202	0.202	0.199	0.245	0.2203	RANDOM	57.512

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]
0.02			-0.18		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.422
r_dihedral_angle_3_deg	20.559
r_dihedral_angle_4_deg	16.138
r_dihedral_angle_1_deg	8.512
r_scangle_it	1.893
r_angle_refined_deg	1.545
r_scbond_it	1.081
r_mcangle_it	0.864
r_mcbond_it	0.476
r_nbtor_refined	0.324
r_nbd_refined	0.158
r_symmetry_hbond_refined	0.144
r_symmetry_vdw_refined	0.143
r_chiral_restr	0.116
r_xyhbond_nbd_refined	0.106
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12222
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
CNS	phasing