3E1N | pdb_00003e1n

Crystal structure of E. coli Bacterioferritin (BFR) after a 65 minute (aerobic) exposure to FE(II) revealing a possible MU-OXO bridge/MU-Hydroxy bridged DIIRON intermediate at the ferroxidase centre. (FE(III)-O-FE(III)-BFR).

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QP7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	298	1.8 M AMMONIUM SULFATE, 0.1 M TRI- SODIUM CITRATE PH 5.0. CRYSTALS OF OF APO-BFR WERE SUBSEQUENTLY SOAKED AEROBICALLY FOR 65 MINUTES IN A SOLUTION CONTAINING FE2+ AND BUFFERED WITH MOPS PH 7 INSTEAD OF CITRATE PH 5. AFTER 65MIN EXPOSURE TO IRON AND AIR, THE CRYSTAL WAS FLASH FROZEN IN LIQUID NITROGEN AND X-RAY DIFFRACTION DATA COLLECTED. SEE PAPER FOR FULL DETAILS., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K, pH 5.00

Crystal Properties
Matthews coefficient	Solvent content
3.47	64.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 207.741	α = 90
b = 207.741	β = 90
c = 142.951	γ = 90

Symmetry
Space Group	P 42 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	CCD			2006-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1		SRS	PX10.1

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	2.8	32.7	98.1	0.17	13.6	11		75629

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)
	2.8	2.95	91.9		0.251	5.2	5.7

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	2QP7	2.8	32.67	71794	3785	98	0.251	0.25	0.2453	0.268	0.2613	EXTENDED FROM THE SAME SET USED IN 2QP7 (APO-BFR)	10.82

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]
-0.74			-0.74		1.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.238
r_dihedral_angle_3_deg	21.763
r_dihedral_angle_4_deg	21.318
r_dihedral_angle_1_deg	4.891
r_scangle_it	3.482
r_scbond_it	2.186
r_angle_refined_deg	1.856
r_mcangle_it	1.208
r_mcbond_it	0.819
r_nbtor_refined	0.32
r_symmetry_hbond_refined	0.309
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.222
r_xyhbond_nbd_refined	0.184
r_chiral_restr	0.149
r_metal_ion_refined	0.048
r_bond_refined_d	0.017
r_gen_planes_refined	0.005
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15912
Nucleic Acid Atoms
Solvent Atoms	246
Heterogen Atoms	374

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling