2Z51 | pdb_00002z51

Crystal structure of Arabidopsis CnfU involved in iron-sulfur cluster biosynthesis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	277	PEG 1000, MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.546	α = 90
b = 57.394	β = 90
c = 61.303	γ = 90

Symmetry
Space Group	P 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	Bruker DIP-6040		2004-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.35	61.31	99.9				34580		26.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.348	1.383	97.97

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 (All)	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	SIRAS	THROUGHOUT	1.35	61.31	32814	1766	99.75	0.13671	0.13671	0.13477	0.14	0.17338	0.14	RANDOM	21.328

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]
-0.08			-0.21		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.698
r_dihedral_angle_4_deg	21.466
r_sphericity_free	14.982
r_dihedral_angle_3_deg	14.004
r_scangle_it	7.891
r_sphericity_bonded	7.332
r_dihedral_angle_1_deg	5.959
r_scbond_it	5.766
r_mcangle_it	4.119
r_rigid_bond_restr	3.389
r_mcbond_it	3.199
r_angle_refined_deg	1.634
r_symmetry_hbond_refined	0.475
r_xyhbond_nbd_refined	0.348
r_nbtor_refined	0.319
r_chiral_restr	0.292
r_symmetry_vdw_refined	0.289
r_nbd_refined	0.27
r_metal_ion_refined	0.139
r_bond_refined_d	0.03
r_symmetry_metal_ion_refined	0.026
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1193
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing