Mass: 40475.816 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: fni, idi / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) References: UniProt: P61615, isopentenyl-diphosphate Delta-isomerase
#2: Chemical
ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
Mass: 458.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H23N4O9P
Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 2.2→50 Å / Num. obs: 88214 / % possible obs: 98.1 % / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.8
Reflection shell
Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 4.7 / % possible all: 99.4
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
MOLREP
phasing
REFMAC
5.5.0109
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→31.62 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.89 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24156
4398
5 %
RANDOM
Rwork
0.20017
-
-
-
obs
0.20223
83363
97.82 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 36.144 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.01 Å2
0 Å2
0 Å2
2-
-
0.01 Å2
0 Å2
3-
-
-
-0.01 Å2
Refinement step
Cycle: LAST / Resolution: 2.2→31.62 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
11232
0
184
467
11883
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.022
0.022
11604
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.945
1.989
15660
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.039
5
1452
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.571
24.569
464
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
19.075
15
2128
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.436
15
64
X-RAY DIFFRACTION
r_chiral_restr
0.164
0.2
1760
X-RAY DIFFRACTION
r_gen_planes_refined
0.009
0.021
8376
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.83
1.5
7200
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.595
2
11584
X-RAY DIFFRACTION
r_scbond_it
2.814
3
4404
X-RAY DIFFRACTION
r_scangle_it
4.734
4.5
4076
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
Refine LS restraints NCS
Refine-ID: X-RAY DIFFRACTION
Ens-ID
Dom-ID
Auth asym-ID
Number
Type
Rms dev position (Å)
Weight position
1
1
A
2735
tightpositional
0.07
0.05
1
1
B
2735
tightpositional
0.08
0.05
1
1
C
2735
tightpositional
0.08
0.05
1
1
D
2735
tightpositional
0.07
0.05
2
2
A
31
tightpositional
0.06
0.05
2
2
B
31
tightpositional
0.05
0.05
2
2
C
31
tightpositional
0.05
0.05
2
2
D
31
tightpositional
0.06
0.05
1
1
A
2735
tightthermal
0.23
0.5
1
1
B
2735
tightthermal
0.23
0.5
1
1
C
2735
tightthermal
0.24
0.5
1
1
D
2735
tightthermal
0.22
0.5
2
2
A
31
tightthermal
0.24
0.5
2
2
B
31
tightthermal
0.25
0.5
2
2
C
31
tightthermal
0.36
0.5
2
2
D
31
tightthermal
0.3
0.5
LS refinement shell
Resolution: 2.199→2.256 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.294
322
-
Rwork
0.254
6121
-
obs
-
-
98.88 %
+
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