Experiment: 5LMC

Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4D02

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	304	1.0 UL OF PROTEIN AT15 MG/ML WITH 0.8 UL OF CRYSTALLIZATION SOLUTION (0.2M NA-CACODYLATE PH 6.5, 0.2 M MG-ACETATE, 20% PEG8000) and 0.2 UL OF 0.1 MOLAR HEXAMINE COBALT (III).

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 150.471	α = 90
b = 150.471	β = 90
c = 95.361	γ = 120

Symmetry
Space Group	P 6 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 315		2008-09-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9722	Diamond	I04

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	1.9	59.07	98.6	0.119	46.5	9.8		49678			24

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2.02	92.7		0.65	1.7	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	FREE R-VALUE	4d02	1.9	59.07	1.35	49678	1648	98.6	0.166	0.166	0.166	0.1376	random selection

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]
-3.8841			-3.8841		7.7682

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.948
f_angle_d	1.068
f_chiral_restr	0.078
f_bond_d	0.015
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3210
Nucleic Acid Atoms
Solvent Atoms	396
Heterogen Atoms	60

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing