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). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999
SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2007 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97901 Å / Relative weight: 1
Reflection
Resolution: 1.9→29.161 Å / Num. obs: 42457 / % possible obs: 100 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 4.8
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured all
Num. unique all
Rsym value
% possible all
1.9-1.95
7.2
0.671
1
22245
3074
0.671
99.8
1.95-2
9.2
0.5
1.5
27644
3018
0.5
100
2-2.06
10.9
0.41
1.9
31843
2916
0.41
100
2.06-2.12
10.9
0.342
1.5
30948
2846
0.342
100
2.12-2.19
10.9
0.265
2.9
30315
2774
0.265
100
2.19-2.27
10.9
0.244
1.1
29074
2673
0.244
100
2.27-2.36
10.9
0.182
4.1
28136
2575
0.182
100
2.36-2.45
10.9
0.156
4.8
27169
2488
0.156
100
2.45-2.56
10.9
0.136
5.4
26210
2404
0.136
100
2.56-2.69
10.8
0.119
5.8
25051
2309
0.119
100
2.69-2.83
10.9
0.102
6.8
23830
2192
0.102
100
2.83-3
10.8
0.087
7.7
22531
2081
0.087
100
3-3.21
10.8
0.078
8.1
21137
1963
0.078
100
3.21-3.47
10.6
0.075
8.1
19460
1830
0.075
100
3.47-3.8
10.5
0.078
7.5
17712
1690
0.078
100
3.8-4.25
10.5
0.07
8.2
16272
1557
0.07
100
4.25-4.91
10.4
0.063
9
14229
1374
0.063
100
4.91-6.01
10.2
0.066
9.2
12164
1197
0.066
100
6.01-8.5
9.7
0.06
9.6
9134
939
0.06
100
8.5-29.161
8.6
0.056
10.2
4795
557
0.056
97.3
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
SCALA
datascaling
PDB_EXTRACT
3
dataextraction
MAR345
CCD
datacollection
MOSFLM
datareduction
Refinement
Method to determine structure: SAD / Resolution: 1.9→29.161 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.168 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.101 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. PGE WERE MODELED AS FRAGMENTS OF PEG-200 FROM THE CRYSTALLIZATION CONDITIONS. 5. RESIDUES 1 AND 306-310 HAVE POOR DENSITY AND WERE NOT MODELED. 6. THERE ARE NUMEROUS SMALL BLOBS OF DIFFERENCE DENSITY THAT WERE NOT MODELED.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.196
2143
5 %
RANDOM
Rwork
0.175
-
-
-
obs
0.176
42439
99.97 %
-
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: 26.102 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.5 Å2
-0.25 Å2
0 Å2
2-
-
-0.5 Å2
0 Å2
3-
-
-
0.75 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→29.161 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2509
0
20
221
2750
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.016
0.022
2707
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1856
X-RAY DIFFRACTION
r_angle_refined_deg
1.543
1.983
3664
X-RAY DIFFRACTION
r_angle_other_deg
1.037
3
4546
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.975
5
353
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.727
24.035
114
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.232
15
475
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.047
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.184
0.2
417
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
3006
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
545
X-RAY DIFFRACTION
r_nbd_refined
0.221
0.2
500
X-RAY DIFFRACTION
r_nbd_other
0.197
0.2
1940
X-RAY DIFFRACTION
r_nbtor_refined
0.181
0.2
1310
X-RAY DIFFRACTION
r_nbtor_other
0.085
0.2
1410
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.141
0.2
187
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.212
0.2
18
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.239
0.2
52
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.214
0.2
16
X-RAY DIFFRACTION
r_mcbond_it
2.21
3
1815
X-RAY DIFFRACTION
r_mcbond_other
0.544
3
690
X-RAY DIFFRACTION
r_mcangle_it
2.946
5
2719
X-RAY DIFFRACTION
r_scbond_it
5.64
8
1119
X-RAY DIFFRACTION
r_scangle_it
7.413
11
934
LS refinement shell
Resolution: 1.9→1.949 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.265
183
-
Rwork
0.211
2881
-
obs
-
3064
99.67 %
Refinement TLS params.
Method: refined / Origin x: 77.102 Å / Origin y: 22.071 Å / Origin z: 0.85 Å
11
12
13
21
22
23
31
32
33
T
-0.0465 Å2
0.0241 Å2
-0.0198 Å2
-
-0.1124 Å2
0.0202 Å2
-
-
-0.0515 Å2
L
0.4431 °2
-0.2363 °2
-0.2112 °2
-
0.6944 °2
0.1637 °2
-
-
0.3109 °2
S
-0.0435 Å °
-0.0184 Å °
-0.033 Å °
-0.0238 Å °
0.0216 Å °
0.1123 Å °
0.0034 Å °
-0.0247 Å °
0.0219 Å °
+
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