- PDB-5o5e: Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosp... -
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Basic information
Entry
Database: PDB / ID: 5o5e
Title
Crystal structure of human UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (DPAGT1) (V264G mutant) in complex with tunicamycin
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→25.87 Å / Cor.coef. Fo:Fc: 0.9076 / Cor.coef. Fo:Fc free: 0.9298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.428 Details: STRUCTURE REFINED WITH BUSTER WITH A SINGLE TLS GROUP. ELECTRON DENSITY MAPS WERE SHARPENED WITH -100A**2 BFACTOR FOR REBUILDING IN COOT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2363
552
5.12 %
RANDOM
Rwork
0.2294
-
-
-
obs
0.2298
10786
99.9 %
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Displacement parameters
Biso mean: 172.25 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-5.492 Å2
0 Å2
0 Å2
2-
-
-5.492 Å2
0 Å2
3-
-
-
10.9839 Å2
Refine analyze
Luzzati coordinate error obs: 0.439 Å
Refinement step
Cycle: 1 / Resolution: 3.4→25.87 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2937
0
104
9
3050
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.009
3117
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1
4238
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
1399
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
43
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
451
HARMONIC
5
X-RAY DIFFRACTION
t_it
3117
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.22
X-RAY DIFFRACTION
t_other_torsion
3.1
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
424
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
3888
SEMIHARMONIC
4
LS refinement shell
Resolution: 3.4→3.8 Å / Total num. of bins used: 5
Rfactor
Num. reflection
% reflection
Rfree
0.2602
147
4.94 %
Rwork
0.2095
2826
-
all
0.2118
2973
-
obs
-
-
99.97 %
Refinement TLS params.
Method: refined / Origin x: 45.6838 Å / Origin y: 49.8451 Å / Origin z: 128.728 Å
11
12
13
21
22
23
31
32
33
T
-0.6971 Å2
-0.1107 Å2
-0.0373 Å2
-
0.2511 Å2
0.2447 Å2
-
-
-0.4151 Å2
L
4.2871 °2
0.9869 °2
-0.6794 °2
-
6.0762 °2
-0.5503 °2
-
-
4.0734 °2
S
-0.2455 Å °
1.0588 Å °
0.6805 Å °
-0.2991 Å °
0.2782 Å °
-0.4952 Å °
-0.3093 Å °
1.1035 Å °
-0.0327 Å °
Refinement TLS group
Selection details: {A|8 - 402}
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