BIOSYNTHETIC PROTEIN / Non heme Fe(II) dioxygenase / cupin
Function / homology
Function and homology information
2-hydroxyethylphosphonate dioxygenase / organic phosphonate biosynthetic process / phosphinothricin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / antibiotic biosynthetic process / ferrous iron binding / protein homodimerization activity / DNA binding / identical protein binding Similarity search - Function
Resolution: 1.8→1.86 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3480 / % possible all: 90.6
-
Processing
Software
Name
Version
Classification
MAR345dtb
datacollection
SHARP
phasing
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.139 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24647
1924
5 %
RANDOM
Rwork
0.20998
-
-
-
obs
0.21182
36648
98.92 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 26.698 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.14 Å2
0 Å2
0 Å2
2-
-
2.73 Å2
0 Å2
3-
-
-
-0.59 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3179
0
13
339
3531
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.007
0.021
3258
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
3
X-RAY DIFFRACTION
r_angle_refined_deg
1.073
1.947
4448
X-RAY DIFFRACTION
r_angle_other_deg
0.564
3
5
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.851
5
414
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.722
22.759
145
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.36
15
475
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.855
15
29
X-RAY DIFFRACTION
r_chiral_restr
0.069
0.2
496
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.02
2539
X-RAY DIFFRACTION
r_gen_planes_other
0
0.02
2
X-RAY DIFFRACTION
r_nbd_refined
0.199
0.2
1413
X-RAY DIFFRACTION
r_nbd_other
0.197
0.2
2
X-RAY DIFFRACTION
r_nbtor_refined
0.296
0.2
2214
X-RAY DIFFRACTION
r_nbtor_other
0.171
0.2
6
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.118
0.2
282
X-RAY DIFFRACTION
r_metal_ion_refined
0.166
0.2
7
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.206
0.2
132
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.144
0.2
38
X-RAY DIFFRACTION
r_mcbond_it
0.676
1.5
2121
X-RAY DIFFRACTION
r_mcbond_other
0.12
1.5
3
X-RAY DIFFRACTION
r_mcangle_it
0.986
2
3310
X-RAY DIFFRACTION
r_scbond_it
1.457
3
1297
X-RAY DIFFRACTION
r_scangle_it
2.286
4.5
1138
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.292
128
-
Rwork
0.255
2431
-
obs
-
-
90.07 %
+
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