2W57

Crystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals structural rearrangement of the DNA-binding domains

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MZB	PDB ENTRIES 1MZB,2FU4
experimental model	PDB	2FU4	PDB ENTRIES 1MZB,2FU4

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.47	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.88	α = 90
b = 88.88	β = 90
c = 85.07	γ = 90

Symmetry
Space Group	P 43 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	RIGAKU SATURN 944			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

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	2.6	18	100	0.13	16.6	8.6		10961

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	2.6	2.74	100		0.6	3.3	8.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRIES 1MZB,2FU4	2.6	62.87	10383	522	99.3	0.218	0.216	0.259	RANDOM

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.475
r_dihedral_angle_4_deg	23.05
r_dihedral_angle_3_deg	16.691
r_dihedral_angle_1_deg	5.467
r_scangle_it	2.383
r_scbond_it	1.455
r_angle_refined_deg	1.215
r_mcangle_it	1.19
r_mcbond_it	0.674
r_xyhbond_nbd_refined	0.321
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.22
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.14
r_chiral_restr	0.069
r_metal_ion_refined	0.064
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2100
Nucleic Acid Atoms
Solvent Atoms	79
Heterogen Atoms	4

Software

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