- PDB-1vku: Crystal structure of Acyl carrier protein (TM0175) from Thermotog... -
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Basic information
Entry
Database: PDB / ID: 1vku
Title
Crystal structure of Acyl carrier protein (TM0175) from Thermotoga maritima at 2.00 A resolution
Components
acyl carrier protein
Keywords
BIOSYNTHETIC PROTEIN / TM0175 / ACYL CARRIER PROTEIN / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics
Resolution: 2→27.02 Å / Num. obs: 6172 / % possible obs: 96.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 33.51 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.8
Reflection shell
Resolution: 2→2.11 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 756 / Rsym value: 0.416 / % possible all: 83.9
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Processing
Software
Name
Version
Classification
MOSFLM
datareduction
SCALA
4.2)
datascaling
autoSHARP
phasing
SOLOMON
phasing
REFMAC
5.2.0001
refinement
CCP4
(SCALA)
datascaling
Refinement
Method to determine structure: MAD / Resolution: 2→27.02 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.87 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.184 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: DENSITY FOR HIS -2, HIS -1, GLU 23, THR 24, ILE 81 AND ASP 82 ARE WEAK
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25276
278
4.5 %
RANDOM
Rwork
0.19696
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-
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obs
0.19954
5871
96.58 %
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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: 32.457 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.54 Å2
0.77 Å2
0 Å2
2-
-
1.54 Å2
0 Å2
3-
-
-
-2.31 Å2
Refinement step
Cycle: LAST / Resolution: 2→27.02 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
683
0
0
45
728
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
700
X-RAY DIFFRACTION
r_angle_refined_deg
1.373
1.977
934
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.297
5
84
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.814
26.364
33
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
16.569
15
153
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
10.859
15
2
X-RAY DIFFRACTION
r_chiral_restr
0.092
0.2
110
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
492
X-RAY DIFFRACTION
r_nbd_refined
0.206
0.2
305
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.15
0.2
36
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.18
0.2
28
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.118
0.2
5
X-RAY DIFFRACTION
r_mcbond_it
1.929
3
439
X-RAY DIFFRACTION
r_mcangle_it
3.03
5
691
X-RAY DIFFRACTION
r_scbond_it
5.825
8
284
X-RAY DIFFRACTION
r_scangle_it
8.631
11
243
LS refinement shell
Resolution: 2→2.108 Å / Total num. of bins used: 10
Rfactor
Num. reflection
% reflection
Rfree
0.292
32
4.27 %
Rwork
0.279
717
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Refinement TLS params.
Method: refined / Origin x: 26.477 Å / Origin y: 17.427 Å / Origin z: 5.629 Å
11
12
13
21
22
23
31
32
33
T
-0.1951 Å2
-0.0124 Å2
0.0067 Å2
-
-0.1781 Å2
0.0218 Å2
-
-
-0.1171 Å2
L
2.0729 °2
0.154 °2
0.2165 °2
-
1.1936 °2
-0.1977 °2
-
-
4.7063 °2
S
-0.0871 Å °
0.0472 Å °
0.057 Å °
-0.013 Å °
0.045 Å °
-0.0433 Å °
-0.1613 Å °
0.1261 Å °
0.0421 Å °
Refinement TLS group
Selection: ALL
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