Mass: 18.015 Da / Num. of mol.: 689 / Source method: isolated from a natural source / Formula: H2O
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Details
Compound details
THE NON-HEME IRON CENTER IS LOCATED AT THE INTERFACE BETWEEN THE A AND B SUBUNIT. THREE CYSTEINE ...THE NON-HEME IRON CENTER IS LOCATED AT THE INTERFACE BETWEEN THE A AND B SUBUNIT. THREE CYSTEINE RESIDUES, ONE SERINE RESIDUE IN THE A SUBUNIT ARE COORDINATED TO THE NON-HEME IRON ATOM. TWO OF THE THREE CYSTEINE RESIDUES (CYS 112 AND CYS 114) ARE POST-TRANSLATIONALLY MODIFIED TO CYSTEINE SULFINIC (112 CYS-SO2H) AND CYSTEINE SULFENIC (114 CYS-SOH) ACIDS. THE SIXTH LIGAND IS AN ENDOGENOUS NO MOLECULE.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.4 Å3/Da / Density % sol: 49 % Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Resolution: 1.7→8 Å / Num. obs: 88965 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 4.08 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.3
Reflection shell
Resolution: 1.7→1.9 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.2 / % possible all: 76.4
Reflection
*PLUS
Num. measured all: 371002
Reflection shell
*PLUS
% possible obs: 76.4 %
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Processing
Software
Name
Version
Classification
DM
modelbuilding
MLPHARE
phasing
X-PLOR
3
refinement
WEIS
datareduction
CCP4
(SCALA)
datascaling
DM
phasing
Refinement
Method to determine structure: MIR / Resolution: 1.7→8 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / σ(F): 2 / Details: ALL ATOMS IN AN ASYMMETRIC UNIT WERE REFINED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.228
-
10 %
RANDOM
Rwork
0.179
-
-
-
obs
0.179
84827
90 %
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Refine analyze
Luzzati coordinate error obs: 0.19 Å
Refinement step
Cycle: LAST / Resolution: 1.7→8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6416
0
35
689
7140
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.013
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
2.7
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
1.99
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.16
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
X-RAY DIFFRACTION
x_mcangle_it
X-RAY DIFFRACTION
x_scbond_it
X-RAY DIFFRACTION
x_scangle_it
LS refinement shell
Resolution: 1.7→1.78 Å / Total num. of bins used: 8
Rfactor
Num. reflection
% reflection
Rfree
0.228
-
10.1 %
Rwork
0.323
7415
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Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PARAM19X.PRO
TOPH19X.PRO
X-RAY DIFFRACTION
2
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_dihedral_angle_d
X-RAY DIFFRACTION
x_dihedral_angle_deg
1.99
X-RAY DIFFRACTION
x_improper_angle_d
X-RAY DIFFRACTION
x_improper_angle_deg
1.16
LS refinement shell
*PLUS
Rfactor obs: 0.323
+
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