8GEP | pdb_00008gep

SULFITE REDUCTASE HEMOPROTEIN NITRATE COMPLEX

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.7		pH 7.7 OXIDIZED CRYSTALS WERE TREATED WITH HYDROXYLAMINE TO FORM THE NITRATE COMPLEX. SIROHEME HAS EITHER FEIII OR FEII AND [4FE-4S] CLUSTER IS +2. THE NITRATE BINDS IN THE ACTIVE SITE BUT DOES NOT COORDINATE THE SIROHEME IRON. THIS IS NAMED HP-NO3 IN THE PRIMARY REFERENCE.

Crystal Properties
Matthews coefficient	Solvent content
2.13	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.8	α = 90
b = 77.4	β = 90
c = 87.8	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	277	IMAGE PLATE	MARRESEARCH		1995-10-19	M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
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	2.2	30	92.8	0.077	12	2.3		22966			16.3

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)
1	2.2	2.4	83.5		0.338	2.1

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB ENTRY 1AOP	2.2	10	2	22130		90.5	0.189	0.189		12.6

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]
-1.28			0.79		0.5

RMS Deviations
Key	Refinement Restraint Deviation
x_angle_deg	1.6
x_bond_d	0.011
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3590
Nucleic Acid Atoms
Solvent Atoms	335
Heterogen Atoms	76

Software

Software
Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MARXDS	data reduction
MARSCALE	data scaling
X-PLOR	phasing