Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300
BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.
Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 1.8 Å3/Da / Density % sol: 32.2 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion / pH: 5.5 Details: 28% PEG3350, 0.1 M Ammonium sulfate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, temperature 291K
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength (Å)
SYNCHROTRON
APS
23-ID-D
1
0.97926
SYNCHROTRON
CHESS
A1
2
0.9777
Detector
Type
ID
Detector
Date
MARMOSAIC 300 mm CCD
1
CCD
Apr 16, 2007
ADSC QUANTUM 210
2
CCD
May 5, 2007
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
0.97926
1
2
0.9777
1
Reflection
Resolution: 1.3→70 Å / Num. obs: 40375 / % possible obs: 96.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.096 / Χ2: 1.795 / Net I/σ(I): 8.2
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
1.3-1.35
3.1
0.28
3089
0.898
74.1
1.35-1.4
4.1
0.276
3777
0.917
90.6
1.4-1.46
5.3
0.252
4074
0.999
97.3
1.46-1.54
6.2
0.211
4147
1.067
99.5
1.54-1.64
6.7
0.176
4181
1.189
100
1.64-1.76
7
0.149
4195
1.383
100
1.76-1.94
7.1
0.123
4176
1.758
100
1.94-2.22
7.2
0.101
4231
2.113
100
2.22-2.8
7.2
0.085
4208
2.516
100
2.8-70
6.9
0.068
4297
3.561
99.7
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Phasing
Phasing
Method: sad
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Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
REFMAC
refmac_5.2.0019
refinement
PDB_EXTRACT
2
dataextraction
ADSC
Quantum
datacollection
Refinement
Method to determine structure: SAD / Resolution: 1.3→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.204 / SU B: 1.025 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.066 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs arp/warp, coot, molprobity were also used in refinement.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.226
2052
5.1 %
RANDOM
Rwork
0.21
-
-
-
all
0.211
-
-
-
obs
-
40353
95.78 %
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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: 7.181 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0.25 Å2
2-
-
-0.13 Å2
0 Å2
3-
-
-
0.26 Å2
Refinement step
Cycle: LAST / Resolution: 1.3→30 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1668
0
27
135
1830
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.021
1747
X-RAY DIFFRACTION
r_bond_other_d
0.003
0.02
1154
X-RAY DIFFRACTION
r_angle_refined_deg
1.317
1.958
2383
X-RAY DIFFRACTION
r_angle_other_deg
0.899
3
2790
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.656
5
218
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.047
22.597
77
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.064
15
255
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
21.258
15
11
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
255
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1973
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
392
X-RAY DIFFRACTION
r_nbd_refined
0.202
0.2
351
X-RAY DIFFRACTION
r_nbd_other
0.19
0.2
1181
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
849
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
838
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.088
0.2
98
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.195
0.2
9
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.25
0.2
43
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.084
0.2
15
X-RAY DIFFRACTION
r_mcbond_it
1.602
2
1155
X-RAY DIFFRACTION
r_mcbond_other
0.526
2
439
X-RAY DIFFRACTION
r_mcangle_it
1.914
3
1704
X-RAY DIFFRACTION
r_scbond_it
1.688
2
777
X-RAY DIFFRACTION
r_scangle_it
2.271
3
676
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 (%)
1.3-1.334
0.272
109
0.262
1914
3066
65.982
1.334-1.371
0.339
128
0.253
2483
3036
86.001
1.371-1.41
0.293
122
0.24
2612
2927
93.406
1.41-1.454
0.236
141
0.227
2630
2850
97.228
1.454-1.501
0.24
139
0.211
2610
2772
99.17
1.501-1.554
0.218
138
0.207
2541
2683
99.851
1.554-1.612
0.22
133
0.203
2433
2566
100
1.612-1.678
0.233
122
0.202
2358
2480
100
1.678-1.752
0.259
132
0.193
2268
2400
100
1.752-1.837
0.22
139
0.202
2155
2294
100
1.837-1.936
0.231
95
0.199
2058
2153
100
1.936-2.053
0.18
105
0.197
1955
2060
100
2.053-2.194
0.195
102
0.195
1837
1939
100
2.194-2.369
0.207
80
0.203
1737
1817
100
2.369-2.594
0.234
94
0.203
1571
1665
100
2.594-2.897
0.232
77
0.21
1449
1527
99.935
2.897-3.34
0.217
61
0.21
1270
1331
100
3.34-4.078
0.201
59
0.2
1083
1142
100
4.078-5.715
0.18
39
0.21
856
896
99.888
5.715-30
0.287
37
0.3
481
525
98.667
+
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