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 (0), FOLLOWED BY THE TARGET SEQUENCE.
Resolution: 1.75→37.113 Å / Num. obs: 23448 / % possible obs: 85.1 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.078 / Χ2: 1.07 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
Diffraction-ID
% possible all
1.75-1.81
1.9
0.322
1105
0.876
1
40.2
1.81-1.89
2.3
0.333
1618
0.93
1
59
1.89-1.97
2.6
0.28
2029
0.953
1
74.9
1.97-2.07
2.9
0.208
2306
1.068
1
84.6
2.07-2.2
3.1
0.182
2589
1.006
1
93.8
2.2-2.38
3.3
0.159
2687
1.1
1
98.2
2.38-2.61
3.5
0.141
2730
1.186
1
99.5
2.61-2.99
3.6
0.103
2770
1.146
1
100
2.99-3.77
3.6
0.071
2776
1.098
1
100
3.77-50
3.5
0.052
2838
0.998
1
99.7
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
MolProbity
3beta29
modelbuilding
SHELX
phasing
REFMAC
5.2.0005
refinement
SCALEPACK
datascaling
PDB_EXTRACT
2
dataextraction
DENZO
datareduction
autoSHARP
phasing
SHELXD
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.75→37.113 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.498 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.132 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THERE IS UNMODELED DENSITY NEAR RESIDUES B26 AND B40. 5. THE NOMINAL RESOLUTION IS 1.90 A WITH 2925 OBSERVED REFLECTIONS BETWEEN 1.90-1.75 (48.5% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT. 6. SULFATE, GLYCEROL, AND ACETATE WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.217
1168
5 %
RANDOM
Rwork
0.173
-
-
-
obs
0.175
23443
84.13 %
-
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: 30.168 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.98 Å2
0 Å2
1.91 Å2
2-
-
-0.16 Å2
0 Å2
3-
-
-
0.49 Å2
Refinement step
Cycle: LAST / Resolution: 1.75→37.113 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2000
0
59
191
2250
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
2175
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1918
X-RAY DIFFRACTION
r_angle_refined_deg
1.274
1.943
2975
X-RAY DIFFRACTION
r_angle_other_deg
0.76
3
4446
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.494
5
266
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
32.202
24.286
105
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
10.888
15
333
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
25.692
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.079
0.2
321
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2403
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
453
X-RAY DIFFRACTION
r_nbd_refined
0.204
0.2
449
X-RAY DIFFRACTION
r_nbd_other
0.167
0.2
1887
X-RAY DIFFRACTION
r_nbtor_refined
0.185
0.2
1058
X-RAY DIFFRACTION
r_nbtor_other
0.082
0.2
1151
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.162
0.2
142
X-RAY DIFFRACTION
r_xyhbond_nbd_other
0.029
0.2
1
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.157
0.2
13
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.266
0.2
39
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.109
0.2
13
X-RAY DIFFRACTION
r_mcbond_it
1.653
3
1384
X-RAY DIFFRACTION
r_mcbond_other
0.402
3
510
X-RAY DIFFRACTION
r_mcangle_it
2.212
5
2085
X-RAY DIFFRACTION
r_scbond_it
3.8
8
1008
X-RAY DIFFRACTION
r_scangle_it
4.683
11
880
LS refinement shell
Resolution: 1.751→1.796 Å / Total num. of bins used: 20
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