3FEZ | pdb_00003fez

Crystal structure of uncharacterized ferredoxin fold protein related to antibiotic biosynthesis monooxygenases (YP_014836.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.10 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	277	0.2000M NH4H2PO3, 20.0000% PEG-3350, No Buffer pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.75	67.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.22	α = 90
b = 73.22	β = 90
c = 214.38	γ = 120

Symmetry
Space Group	P 61 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	MAR MAR300	Adjustable focusing mirrors in K-B geometry	2008-10-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	0.94645,0.97966	APS	23-ID-B

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	2.1	28.976	97.9	0.155				20290		-3	36.004

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	2.1	2.17	91.5		0.011	1.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.1	28.976	20282	1039	97.87	0.204	0.203	0.21	0.227	0.23	RANDOM	53.552

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]
0.07	0.04		0.07		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.369
r_dihedral_angle_4_deg	18.94
r_dihedral_angle_3_deg	12.262
r_dihedral_angle_1_deg	4.333
r_scangle_it	2.343
r_scbond_it	1.72
r_angle_refined_deg	1.289
r_mcangle_it	1.242
r_mcbond_it	0.843
r_angle_other_deg	0.771
r_symmetry_vdw_refined	0.239
r_nbd_refined	0.235
r_symmetry_vdw_other	0.218
r_nbtor_refined	0.192
r_nbd_other	0.184
r_symmetry_hbond_refined	0.182
r_xyhbond_nbd_refined	0.165
r_mcbond_other	0.144
r_nbtor_other	0.089
r_chiral_restr	0.082
r_xyhbond_nbd_other	0.035
r_bond_refined_d	0.017
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1360
Nucleic Acid Atoms
Solvent Atoms	84
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing