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.
Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Sequence details
REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal grow
Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: NANODROP, 40.0% 2-ethoxyethanol, 0.05M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.85→28.772 Å / Num. obs: 22750 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8.99 % / Biso Wilson estimate: 16.68 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.16
Reflection shell
Resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
Diffraction-ID
% possible all
1.85-1.92
0.791
2
20840
4428
1
98
1.92-1.99
0.676
2.4
18943
3980
1
100
1.99-2.08
0.513
3.2
20118
4219
1
100
2.08-2.19
0.373
4.3
20877
4372
1
100
2.19-2.33
0.305
5.2
21081
4412
1
100
2.33-2.51
0.246
6.5
20605
4303
1
100
2.51-2.76
0.183
8.4
20446
4276
1
100
2.76-3.16
0.126
11.5
20635
4316
1
100
3.16-3.98
0.075
17.3
20474
4310
1
100
3.98-28.772
0.059
20.5
20469
4329
1
99.7
-
Phasing
Phasing
Method: MAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SOLVE
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3
dataextraction
ADSC
Quantum
datacollection
XDS
datareduction
Refinement
Method to determine structure: MAD / Resolution: 1.85→28.772 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.371 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.109 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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. CALCIUM IONS, ACETATE (ACT) AND 2-ETHOXYETHANOL (ETX) MODELED ARE PRESENT IN THE CRYSTALLIZATION/CRYO CONDITIONS. 5. RAMACHANDRAN OUTLIER A71 AND ROTAMER OUTLIER A197 ARE SUPPORTED BY CLEARLY DEFINED DENSITY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.195
1768
7.8 %
RANDOM
Rwork
0.158
-
-
-
obs
0.161
22714
99.94 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 16.365 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.45 Å2
0.23 Å2
0 Å2
2-
-
0.45 Å2
0 Å2
3-
-
-
-0.68 Å2
Refinement step
Cycle: LAST / Resolution: 1.85→28.772 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1520
0
18
230
1768
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
1611
X-RAY DIFFRACTION
r_bond_other_d
0.002
0.02
1099
X-RAY DIFFRACTION
r_angle_refined_deg
1.3
1.961
2197
X-RAY DIFFRACTION
r_angle_other_deg
0.925
3
2677
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.519
5
203
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.816
23.514
74
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.839
15
264
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
22.952
15
12
X-RAY DIFFRACTION
r_chiral_restr
0.075
0.2
245
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
1785
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
337
X-RAY DIFFRACTION
r_nbd_refined
0.218
0.2
334
X-RAY DIFFRACTION
r_nbd_other
0.201
0.2
1166
X-RAY DIFFRACTION
r_nbtor_refined
0.184
0.2
791
X-RAY DIFFRACTION
r_nbtor_other
0.086
0.2
774
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.166
0.2
144
X-RAY DIFFRACTION
r_metal_ion_refined
0.184
0.2
5
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.248
0.2
4
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.325
0.2
47
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.188
0.2
20
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
0.036
0.2
1
X-RAY DIFFRACTION
r_mcbond_it
1.845
3
1014
X-RAY DIFFRACTION
r_mcbond_other
0.495
3
383
X-RAY DIFFRACTION
r_mcangle_it
2.735
5
1582
X-RAY DIFFRACTION
r_scbond_it
4.549
8
695
X-RAY DIFFRACTION
r_scangle_it
6.145
11
608
LS refinement shell
Resolution: 1.85→1.9 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.28
127
-
Rwork
0.21
1522
-
all
-
1649
-
obs
-
-
99.94 %
+
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