2JI3 | pdb_00002ji3

X-ray structure of the iron-peroxide intermediate of superoxide reductase (E114A mutant) from Desulfoarculus baarsii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VZI	PDB ENTRY 1VZI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	293	16 % PEG 4000, 100 MM TRIS/HNO3 PH9.0, 0.2 M CA(NO3)2 AND 25 MG/ML PROTEIN MIXED 1:1, HANGING DROP VAPOUR DIFFUSION, 20C, pH 9.00

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.45	α = 90
b = 82.9	β = 90
c = 202.66	γ = 90

Symmetry
Space Group	I 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	ADSC CCD	MIRRORS	2006-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	1.95	47.1	97.8	0.09	10.27	4		42838		-3	16.8

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	1.94	2.06	94.7		0.6	2.09	3.7

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	PDB ENTRY 1VZI	1.95	47.13	42472	2147	98.4	0.217	0.217	0.21	0.249	0.24	RANDOM	35.2

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]
1.3			-6.35		5.05

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	26.8
c_scangle_it	3.07
c_mcangle_it	2.23
c_scbond_it	2.05
c_angle_deg	1.5
c_mcbond_it	1.41
c_improper_angle_d	0.77
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3899
Nucleic Acid Atoms
Solvent Atoms	309
Heterogen Atoms	22

Software

Software
Software Name	Purpose
CNS	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing