Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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.
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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: 2.14 Å3/Da / Density % sol: 42.59 % Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND .
Crystal grow
Temperature: 277 K / pH: 9 Details: 30.0000% PEG-6000, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution: 1.8→29.44 Å / Num. obs: 37793 / % possible obs: 91.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.63 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.36
Reflection shell
Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.4 / % possible all: 91.3
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Phasing
Phasing
Method: MAD
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Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.006
dataextraction
XDS
datareduction
SHELXD
phasing
autoSHARP
phasing
Refinement
Method to determine structure: MAD / Resolution: 1.8→29.44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.519 / SU ML: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.155 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.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. 3.1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 4.PYRIDOXAL PHOSPHATE IN DUAL CONFORMATION AS FREE PLP AND COVALENTLY ATTACHED TO LYS288 (LLP) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON DIFFERENCE DENSITY AND OMIT MAPS AND STRUCTURAL SIMILARITY TO PLP-DEPENDENT AMINOTRANSFERASES. 5.RESIDUE ALA287 IS PRESENT IN THE VICINITY OF THE PUTATIVE ACTIVE SITE AND IS A RAMACHANDRAN OUTLIER. THIS COULD HAVE SOME FUNCTIONAL SIGNIFICANCE.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.254
1896
5 %
RANDOM
Rwork
0.205
-
-
-
obs
0.208
37767
96.5 %
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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: 26.22 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.46 Å2
0 Å2
0.65 Å2
2-
-
-2.06 Å2
0 Å2
3-
-
-
3.86 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.44 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3509
0
36
313
3858
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.017
0.022
3675
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
2449
X-RAY DIFFRACTION
r_angle_refined_deg
1.737
1.965
4997
X-RAY DIFFRACTION
r_angle_other_deg
1.06
3
5971
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.024
5
477
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
33.163
24.085
164
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
12.074
15
590
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.294
15
22
X-RAY DIFFRACTION
r_chiral_restr
0.106
0.2
549
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
4157
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
744
X-RAY DIFFRACTION
r_nbd_refined
0.202
0.2
787
X-RAY DIFFRACTION
r_nbd_other
0.191
0.2
2608
X-RAY DIFFRACTION
r_nbtor_refined
0.178
0.2
1745
X-RAY DIFFRACTION
r_nbtor_other
0.088
0.2
1770
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.193
0.2
287
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.216
0.2
33
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.186
0.2
114
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.214
0.2
32
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
1.278
2
2579
X-RAY DIFFRACTION
r_mcbond_other
0.295
2
957
X-RAY DIFFRACTION
r_mcangle_it
1.757
3
3664
X-RAY DIFFRACTION
r_scbond_it
1.168
2
1527
X-RAY DIFFRACTION
r_scangle_it
1.741
3
1321
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.8→1.85 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.395
141
-
Rwork
0.339
2560
-
obs
-
-
94.34 %
+
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