Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2009
Radiation
ID
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
ID
Wavelength (Å)
Relative weight
1
0.97946
1
2
1.07205
1
Reflection
Redundancy: 4.3 % / Av σ(I) over netI: 16.9 / Number: 58756 / Rmerge(I) obs: 0.093 / Χ2: 5.66 / D res high: 2 Å / D res low: 50 Å / Num. obs: 13539 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)
Lowest resolution (Å)
% possible obs (%)
ID
Rmerge(I) obs
Chi squared
Redundancy
5.43
50
99.4
1
0.085
22.605
4.4
4.31
5.43
100
1
0.072
15.661
4.6
3.76
4.31
100
1
0.07
9.477
4.7
3.42
3.76
99.9
1
0.07
7.594
4.6
3.17
3.42
100
1
0.076
6.356
4.7
2.99
3.17
100
1
0.086
5.755
4.7
2.84
2.99
100
1
0.1
4.887
4.7
2.71
2.84
100
1
0.111
4.163
4.7
2.61
2.71
100
1
0.115
3.773
4.7
2.52
2.61
100
1
0.127
3.37
4.7
2.44
2.52
100
1
0.141
2.936
4.6
2.37
2.44
99.9
1
0.145
2.539
4.5
2.31
2.37
99.9
1
0.169
2.14
4.4
2.25
2.31
99.4
1
0.193
2.302
4.3
2.2
2.25
99.4
1
0.204
2.778
4.2
2.15
2.2
98.8
1
0.198
1.906
4
2.11
2.15
98.2
1
0.209
1.728
3.8
2.07
2.11
96.4
1
0.245
1.888
3.7
2.03
2.07
94.3
1
0.243
2.273
3.3
2
2.03
91.6
1
0.261
1.533
3.2
Reflection
Resolution: 1.5→50 Å / Num. obs: 31015 / % possible obs: 98.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.042 / Χ2: 1.371 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.5-1.53
2.5
0.239
1356
1.405
1,2
87.5
1.53-1.55
2.7
0.221
1481
1.117
1,2
93.4
1.55-1.58
3.1
0.213
1483
1.199
1,2
96.7
1.58-1.62
3.3
0.199
1554
1.258
1,2
98.6
1.62-1.65
3.6
0.196
1541
1.26
1,2
99.8
1.65-1.69
3.9
0.186
1548
1.432
1,2
99.7
1.69-1.73
4.1
0.186
1575
1.246
1,2
100
1.73-1.78
4.7
0.176
1540
1.247
1,2
100
1.78-1.83
5.4
0.172
1563
1.19
1,2
100
1.83-1.89
6.3
0.155
1576
1.206
1,2
100
1.89-1.96
7
0.124
1573
1.224
1,2
100
1.96-2.04
7.3
0.1
1554
1.288
1,2
100
2.04-2.13
7.5
0.086
1583
1.386
1,2
100
2.13-2.24
7.5
0.074
1569
1.5
1,2
100
2.24-2.38
7.5
0.061
1560
1.466
1,2
100
2.38-2.56
7.6
0.055
1570
1.484
1,2
100
2.56-2.82
7.6
0.047
1578
1.534
1,2
100
2.82-3.23
7.6
0.035
1587
1.495
1,2
100
3.23-4.07
7.5
0.028
1589
1.446
1,2
100
4.07-50
7.2
0.025
1635
1.422
1,2
99.9
-
Phasing
Phasing
Method: sad
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
REFMAC
refmac_5.5.0102
refinement
PDB_EXTRACT
3.005
dataextraction
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.211 / SU B: 1.548 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: A POTASSIUM HEXAIODOPLATIN-(IV)-ATE DERIVATIVE WAS USED FOR PHASING. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY. ARP/WARP, COOT, MOLPROBITY WERE ALSO USED DURING REFINEMENT.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.257
1038
3.4 %
THIN SHELLS (SFTOOLS)
Rwork
0.207
-
-
-
obs
0.209
30969
98.74 %
-
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: 15.078 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.24 Å2
0 Å2
-0.49 Å2
2-
-
-0.45 Å2
0 Å2
3-
-
-
0.12 Å2
Refinement step
Cycle: LAST / Resolution: 1.5→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1486
0
8
130
1624
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
1609
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1046
X-RAY DIFFRACTION
r_angle_refined_deg
1.59
1.976
2198
X-RAY DIFFRACTION
r_angle_other_deg
0.874
3
2621
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.457
5
219
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
40.59
26.986
73
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.894
15
318
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
6.092
15
2
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
269
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
1789
X-RAY DIFFRACTION
r_gen_planes_other
0.002
0.02
289
X-RAY DIFFRACTION
r_mcbond_it
1.192
1.5
991
X-RAY DIFFRACTION
r_mcbond_other
0.309
1.5
400
X-RAY DIFFRACTION
r_mcangle_it
2.134
2
1623
X-RAY DIFFRACTION
r_scbond_it
3.128
3
618
X-RAY DIFFRACTION
r_scangle_it
5.052
4.5
561
LS refinement shell
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Num. reflection all
% reflection obs (%)
1.5-1.54
0
0.305
2047
2301
88.961
1.54-1.582
0.294
102
0.272
2044
2239
95.846
1.582-1.628
0.313
89
0.246
2064
2178
98.852
1.628-1.678
0.253
97
0.24
2024
2128
99.671
1.678-1.732
0.284
87
0.219
1968
2058
99.854
1.732-1.793
0.257
61
0.215
1914
1979
99.798
1.793-1.861
0.256
64
0.202
1855
1921
99.896
1.861-1.936
0.23
20
0.205
1836
1859
99.839
1.936-2.022
0.253
83
0.193
1682
1768
99.83
2.022-2.12
0.234
69
0.193
1641
1710
100
2.12-2.234
0.271
48
0.195
1557
1605
100
2.234-2.369
0.19
44
0.186
1505
1549
100
2.369-2.531
0.214
36
0.197
1380
1416
100
2.531-2.732
0.218
42
0.194
1310
1352
100
2.732-2.991
0.316
52
0.222
1201
1253
100
2.991-3.34
0.245
36
0.215
1087
1123
100
3.34-3.848
0.265
18
0.196
985
1003
100
3.848-4.694
0.224
55
0.165
797
852
100
4.694-6.559
0.31
14
0.233
660
674
100
6.559-30
0.331
21
0.252
374
395
100
+
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