Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Sequence details
THE COMPLETE SEQUENCE OF THE CONSTRUCT USED FOR CRYSTALLIZATION IS: ...THE COMPLETE SEQUENCE OF THE CONSTRUCT USED FOR CRYSTALLIZATION IS: MHHHHHHSSGRENLYFQGSSPPSSDFAKEEVIGMVTRAHKDTFMYNQEQQENVPIDGFS QNENKNSYLCNTGGRMHLVCPMSKSPYVDPHKSGHEIWEEFSMSFTPAVKEVVEFAKRI PGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHSMGAGDL LNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIM KNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFKVHP, FROM WHICH MHHHHHHSSGRENLYFQG IS AN N-TERMINAL EXPRESSION TAG FOLLOWED BY THE SEQUENCE OF A FUSION PROTEIN, CONTAINING RESIDUES 241-274 OF UNIPROT ENTRY Q14995 (NR1D2_HUMAN): SSPPSSDFAKEEVIGMVTRAHKDTFMYNQEQQEN, AND RESIDUES 358-579 OF UNIPROT ENTRY Q14995 (NR1D2_HUMAN): VPIDGFSQNENKNSYLCNTGGRMHLVCPMSKSPYVDPHKSGHEIWEEFSMSFTPAVKEV VEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLH SMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIR ALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFKVHP. AUTHORS STATE THAT THE PROTEIN SAMPLE WAS MIXED WITH 1:2000 (W/W, PROTEASE TO PROTEIN) RATIO WITH TRYPSIN DURING CONCENTRATION, WHICH EVIDENTLY CLEAVED OFF MANY OF N-TERMINAL RESIDUES OF THE PROTEIN PRIOR TO CRYSTAL FORMATION. THE PRECISE LOCATION OF THE CLEAVAGE SITE HAS NOT BEEN DETERMINED. THEREFORE, THE SEQUENCE INFORMATION, AS WELL AS THE VALUES OF MATTHEWS COEFFICIENT AND SOLVENT CONTENT ARE BASED ON THE CHAIN LENGTH STARTING FROM THE FIRST VISIBLE N-TERMINAL RESIDUE IN ELECTRON DENSITY.
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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: 2.69 Å3/Da / Density % sol: 54.29 % Description: THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS. PROTEIN SAMPLE WAS MIXED WITH 1:2000 (W/W, PROTEASE TO PROTEIN) RATIO WITH TRYPSIN DURING CONCENTRATION. THE MATTHEWS COEFFICIENT ...Description: THE CRYSTAL WAS OBTAINED BY IN SITU PROTEOLYSIS. PROTEIN SAMPLE WAS MIXED WITH 1:2000 (W/W, PROTEASE TO PROTEIN) RATIO WITH TRYPSIN DURING CONCENTRATION. THE MATTHEWS COEFFICIENT CALCULATED BASED ON THE CONSTRUCTED SEQUENCE IS 1.94, AND SOLVENT CONTENT 36.7%. THE VALUES SHOWN IN FILE ARE CALCULATED BASED ON THE SEQUENCE STARTING FROM THE FIRST VISIBLE N-TERMINAL RESIDUE IN ELECTRON DENSITY, THEREFORE THEY MAY NOT BE ACCURATE.
Crystal grow
Temperature: 297 K / Method: vapor diffusion / pH: 7.6 Details: 1.6 M Ammonium sulfate, 0.1 M Na Hepes pH 7.6, 4% Jeffamine M-600, VAPOR DIFFUSION, temperature 297K
Resolution: 1.9→1.93 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 5.46 / Num. unique all: 986 / Rsym value: 0.453 / % possible all: 100
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Processing
Software
Name
Version
Classification
REFMAC
5.2.0019
refinement
HKL-3000
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
SOLVE
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.9→40.56 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.679 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.147 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program COOT 0.3.3 has also been used in refinement
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.23541
1020
5.1 %
RANDOM
Rwork
0.19704
-
-
-
all
0.19899
19007
-
-
obs
0.19899
19007
99.57 %
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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: 25.471 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.15 Å2
0 Å2
0 Å2
2-
-
-0.3 Å2
0 Å2
3-
-
-
0.16 Å2
Refinement step
Cycle: LAST / Resolution: 1.9→40.56 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
1571
0
43
157
1771
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.014
0.022
1654
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.426
2.047
2254
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.73
5
203
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
31.759
24.429
70
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.663
15
290
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.069
15
8
X-RAY DIFFRACTION
r_chiral_restr
0.099
0.2
250
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.02
1239
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.208
0.2
838
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.305
0.2
1162
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.173
0.2
111
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
0.22
0.2
37
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.253
0.2
14
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
1.596
1.5
1027
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.84
2
1625
X-RAY DIFFRACTION
r_scbond_it
3.337
3
695
X-RAY DIFFRACTION
r_scangle_it
5.029
4.5
627
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 1.9→1.95 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.259
72
-
Rwork
0.205
1391
-
obs
-
-
99.93 %
+
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