- PDB-7rm7: The X-ray crystal structure of the N-terminal domain of Staphyloc... -
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Basic information
Entry
Database: PDB / ID: 7rm7
Title
The X-ray crystal structure of the N-terminal domain of Staphylococcus aureus Fatty Acid Kinase A (FakA, residues 1-208) in complex with ADP to 1.025 Angstrom resolution
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.025→34.24 Å / Num. obs: 95789 / % possible obs: 95.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 8.3 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Net I/σ(I): 19.6
Reflection shell
Resolution: 1.025→1.04 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3447 / CC1/2: 0.65 / Rpim(I) all: 0.396 / % possible all: 70.5
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0267
refinement
XDS
datareduction
Aimless
datascaling
SHELXDE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.025→34.24 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.911 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.022 / ESU R Free: 0.024 Details: Phasing was performed using this data set as a remote wavelength coupled with the SAD data from a cobalt-derivatized crystal (PDB ID 7RZK). Hydrogens have been used if present in the input file
Rfactor
Num. reflection
% reflection
Rfree
0.1441
4782
4.996 %
Rwork
0.1177
90938
-
all
0.119
-
-
obs
-
95720
95.158 %
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parameters
Biso mean: 16.035 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.134 Å2
-0 Å2
-0 Å2
2-
-
-0.38 Å2
0 Å2
3-
-
-
1.514 Å2
Refinement step
Cycle: LAST / Resolution: 1.025→34.24 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1659
0
38
361
2058
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.012
1906
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.017
1814
X-RAY DIFFRACTION
r_angle_refined_deg
2.046
1.623
2605
X-RAY DIFFRACTION
r_angle_other_deg
0.67
1.565
4219
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.361
5
265
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.682
26.173
81
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.704
15
349
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
28.729
15
4
X-RAY DIFFRACTION
r_chiral_restr
0.103
0.2
251
X-RAY DIFFRACTION
r_gen_planes_refined
0.013
0.02
2298
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
393
X-RAY DIFFRACTION
r_nbd_refined
0.274
0.2
495
X-RAY DIFFRACTION
r_symmetry_nbd_other
0.192
0.2
1701
X-RAY DIFFRACTION
r_nbtor_refined
0.182
0.2
1000
X-RAY DIFFRACTION
r_symmetry_nbtor_other
0.07
0.2
926
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.258
0.2
229
X-RAY DIFFRACTION
r_metal_ion_refined
0.092
0.2
7
X-RAY DIFFRACTION
r_symmetry_nbd_refined
0.43
0.2
30
X-RAY DIFFRACTION
r_nbd_other
0.292
0.2
96
X-RAY DIFFRACTION
r_symmetry_xyhbond_nbd_refined
0.29
0.2
53
X-RAY DIFFRACTION
r_mcbond_it
5.568
1.151
1000
X-RAY DIFFRACTION
r_mcbond_other
5.569
1.149
999
X-RAY DIFFRACTION
r_mcangle_it
6.157
1.707
1285
X-RAY DIFFRACTION
r_mcangle_other
6.155
1.708
1286
X-RAY DIFFRACTION
r_scbond_it
6.263
1.532
906
X-RAY DIFFRACTION
r_scbond_other
6.263
1.532
906
X-RAY DIFFRACTION
r_scangle_it
7.493
2.156
1320
X-RAY DIFFRACTION
r_scangle_other
7.49
2.156
1321
X-RAY DIFFRACTION
r_lrange_it
8.631
17.912
2424
X-RAY DIFFRACTION
r_lrange_other
8.007
15.916
2319
X-RAY DIFFRACTION
r_rigid_bond_restr
14.257
3
3720
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.025-1.052
0.312
261
0.293
5081
X-RAY DIFFRACTION
72.6407
1.052-1.08
0.229
289
0.214
6117
X-RAY DIFFRACTION
89.2325
1.08-1.112
0.167
333
0.157
6335
X-RAY DIFFRACTION
95.6671
1.112-1.146
0.151
335
0.141
6164
X-RAY DIFFRACTION
96.0396
1.146-1.183
0.153
312
0.134
6055
X-RAY DIFFRACTION
96.6601
1.183-1.225
0.129
329
0.123
5841
X-RAY DIFFRACTION
96.7995
1.225-1.271
0.159
301
0.122
5677
X-RAY DIFFRACTION
97.3774
1.271-1.323
0.148
292
0.117
5501
X-RAY DIFFRACTION
97.5417
1.323-1.382
0.129
274
0.115
5299
X-RAY DIFFRACTION
97.9782
1.382-1.449
0.151
262
0.111
5078
X-RAY DIFFRACTION
98.2882
1.449-1.528
0.134
242
0.106
4900
X-RAY DIFFRACTION
98.4303
1.528-1.62
0.13
241
0.099
4572
X-RAY DIFFRACTION
98.708
1.62-1.732
0.135
218
0.1
4398
X-RAY DIFFRACTION
98.9496
1.732-1.87
0.136
212
0.109
4077
X-RAY DIFFRACTION
98.9845
1.87-2.049
0.122
233
0.097
3744
X-RAY DIFFRACTION
99.3753
2.049-2.29
0.118
176
0.094
3414
X-RAY DIFFRACTION
99.281
2.29-2.643
0.122
156
0.095
3063
X-RAY DIFFRACTION
99.5054
2.643-3.234
0.14
160
0.106
2565
X-RAY DIFFRACTION
99.163
3.234-4.563
0.143
93
0.112
2012
X-RAY DIFFRACTION
96.7371
4.563-34.24
0.254
63
0.215
1045
X-RAY DIFFRACTION
86.1586
Refinement TLS params.
Method: refined / Origin x: 14.9801 Å / Origin y: 5.2362 Å / Origin z: -12.5135 Å
11
12
13
21
22
23
31
32
33
T
0.0196 Å2
0.0006 Å2
-0.0002 Å2
-
0.0153 Å2
-0.0009 Å2
-
-
0.0005 Å2
L
0.0655 °2
0.0079 °2
0.02 °2
-
0.0374 °2
-0.0074 °2
-
-
0.0965 °2
S
0.0009 Å °
0.005 Å °
-0.0057 Å °
-0.0006 Å °
0.0014 Å °
0.0002 Å °
0.0025 Å °
0.0033 Å °
-0.0023 Å °
Refinement TLS group
Selection: ALL
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