- PDB-2f1l: CRYSTAL STRUCTURE OF A PUTATIVE 16S RIBOSOMAL RNA PROCESSING PROT... -
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Basic information
Entry
Database: PDB / ID: 2f1l
Title
CRYSTAL STRUCTURE OF A PUTATIVE 16S RIBOSOMAL RNA PROCESSING PROTEIN RIMM (PA3744) FROM PSEUDOMONAS AERUGINOSA AT 2.46 A RESOLUTION
Components
16S rRNA processing protein
Keywords
UNKNOWN FUNCTION / 16S RRNA PROCESSING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information
rRNA processing / ribosome binding / ribosomal small subunit biogenesis / ribosome / cytoplasm Similarity search - Function
Resolution: 2.4→26.76 Å / Num. obs: 9930 / % possible obs: 98.9 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 6
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Rsym value
% possible all
2.46-2.52
4.6
0.752
1
631
0.752
88.4
2.52-2.59
5.2
0.574
1.3
690
0.574
97.4
2.59-2.67
5.6
0.422
1.5
703
0.422
100
2.67-2.75
5.6
0.312
2.4
665
0.312
100
2.75-2.84
5.5
0.244
3.1
660
0.244
100
2.84-2.94
5.5
0.211
3.5
622
0.211
100
2.94-3.05
5.6
0.166
4.4
613
0.166
100
3.05-3.18
5.6
0.118
6.1
589
0.118
100
3.18-3.32
5.5
0.099
6.8
569
0.099
100
3.32-3.48
5.5
0.088
7.4
557
0.088
100
3.48-3.67
5.5
0.069
9.2
506
0.069
100
3.67-3.89
5.5
0.067
9.4
483
0.067
100
3.89-4.16
5.5
0.056
9.2
472
0.056
100
4.16-4.49
5.4
0.058
10.7
443
0.058
100
4.49-4.92
5.4
0.055
10.9
393
0.055
100
4.92-5.5
5.3
0.062
10
369
0.062
100
5.5-6.35
5.1
0.071
8.5
329
0.071
100
6.35-7.78
5
0.068
8.2
281
0.068
100
7.78-11
4.6
0.054
10.9
226
0.054
100
11-26.76
4.1
0.061
8
129
0.061
94.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0005
refinement
SCALA
datascaling
PDB_EXTRACT
1.601
dataextraction
MOSFLM
datareduction
CCP4
(SCALA)
datascaling
SOLVE
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.46→26.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.915 / SU B: 13.807 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.229 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ELECTRON DENSITY BETWEEN RESIDUE 95 AND RESIDUE 101 IS DISORDERED AND NO MODEL WAS BUILT. 3. THE UNIDEFINED ELECTRON DENISTY NEAR ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE ELECTRON DENSITY BETWEEN RESIDUE 95 AND RESIDUE 101 IS DISORDERED AND NO MODEL WAS BUILT. 3. THE UNIDEFINED ELECTRON DENISTY NEAR THE DOMAIN AND DIMER INTERFACT WAS MODELED AS TWO UNL, UNKNOWN LIGAND.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.237
476
4.8 %
RANDOM
Rwork
0.175
-
-
-
obs
0.17732
9433
98.71 %
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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: MASK
Displacement parameters
Biso mean: 35.483 Å2
Baniso -1
Baniso -2
Baniso -3
1-
3.06 Å2
1.53 Å2
0 Å2
2-
-
3.06 Å2
0 Å2
3-
-
-
-4.59 Å2
Refinement step
Cycle: LAST / Resolution: 2.46→26.8 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1283
0
37
44
1364
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
1359
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1258
X-RAY DIFFRACTION
r_angle_refined_deg
1.702
1.983
1842
X-RAY DIFFRACTION
r_angle_other_deg
0.816
3
2910
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.838
5
172
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
39.487
23.906
64
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.184
15
233
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.484
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
203
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1522
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
274
X-RAY DIFFRACTION
r_nbd_refined
0.207
0.2
210
X-RAY DIFFRACTION
r_nbd_other
0.192
0.2
1283
X-RAY DIFFRACTION
r_nbtor_refined
0.18
0.2
674
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
910
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.202
0.2
80
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.174
0.2
8
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.21
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.121
0.2
10
X-RAY DIFFRACTION
r_mcbond_it
2.4
3
862
X-RAY DIFFRACTION
r_mcbond_other
0.501
3
347
X-RAY DIFFRACTION
r_mcangle_it
2.964
5
1331
X-RAY DIFFRACTION
r_scbond_it
6.2
8
579
X-RAY DIFFRACTION
r_scangle_it
7.835
11
508
LS refinement shell
Resolution: 2.46→2.524 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.311
32
-
Rwork
0.334
595
-
obs
-
-
86.72 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
3.0589
-1.9162
-0.6824
3.8467
2.4374
5.0595
-0.1238
-0.0641
-0.4407
0.1912
-0.1506
0.5393
0.2583
-0.5721
0.2744
0.1506
-0.0603
0.019
0.2221
-0.0082
0.1534
0.0498
37.8744
8.4637
2
3.9162
-2.0461
1.3738
4.6786
-1.5565
4.4096
0.2358
0.3645
-0.1245
-0.571
-0.2555
-0.0371
0.0938
-0.0484
0.0196
0.2169
0.0035
-0.008
0.1822
-0.0336
0.0597
14.9422
31.5484
-12.9114
Refinement TLS group
Refine-ID: X-RAY DIFFRACTION / Selection: all / Auth asym-ID: A / Label asym-ID: A
ID
Refine TLS-ID
Auth seq-ID
Label seq-ID
1
1
7 - 95
19 - 107
2
2
101 - 175
113 - 187
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