Num. of mol.: 11 / Source method: obtained synthetically
Sequence details
THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY ...THE PROTEIN USED FOR CRYSTALLIZATION CONTAINED AMINO-ACIDS AS GIVEN IN DBREF. THIS PROTEIN LIKELY DEGRADED IN THE PRESENCE TRYPSIN TO A TRUNCATED SPECIES DURING THE CRYSTALLIZATION EXPERIMENT. THEREFORE, CALCULATED VM AND VS VALUES ARE BASED ON AN ESTIMATE. THE AUTHORS ASSUMED RESIDUES 890 TO 1205 TO BE PRESENT.
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
-
Sample preparation
Crystal
Density Matthews: 2.4 Å3/Da / Density % sol: 48.6 %
Crystal grow
Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% w/v PEG 3350, 0.2M lithium sulfate, 0.1M HEPES pH 7.5. 1:100 trypsin was also added. vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP
Resolution: 2.8→30 Å / Num. obs: 9116 / % possible obs: 99.8 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.142 / Χ2: 1.237 / Net I/σ(I): 5.5
Reflection shell
Resolution (Å)
Redundancy (%)
Rmerge(I) obs
Num. unique all
Χ2
% possible all
2.8-2.85
6.3
0.469
434
0.807
96.9
2.85-2.9
7.3
0.435
441
0.784
100
2.9-2.96
7.2
0.342
461
0.775
100
2.96-3.02
7.3
0.334
429
0.791
100
3.02-3.08
7.2
0.295
446
0.808
100
3.08-3.15
7.2
0.25
436
0.831
100
3.15-3.23
7.1
0.215
466
0.867
100
3.23-3.32
7.2
0.197
429
0.931
100
3.32-3.42
7.2
0.177
450
0.878
100
3.42-3.53
7.1
0.153
458
1.141
100
3.53-3.65
7.1
0.14
450
1.074
100
3.65-3.8
7.1
0.132
449
1.175
100
3.8-3.97
7
0.117
450
1.335
100
3.97-4.18
7
0.116
458
1.519
99.8
4.18-4.44
6.9
0.111
462
1.683
100
4.44-4.78
6.9
0.098
463
1.794
100
4.78-5.26
6.7
0.098
451
1.447
100
5.26-6.02
6.5
0.117
471
1.308
100
6.02-7.56
6.7
0.102
486
1.55
100
7.56-30
6.1
0.071
526
3.287
100
-
Phasing
Phasing
Method: mad
-
Processing
Software
Name
Version
Classification
NB
DENZO
datareduction
SCALEPACK
datascaling
SHELX
phasing
RESOLVE
phasing
PDB_EXTRACT
3.005
dataextraction
SBC-Collect
datacollection
HKL-3000
datareduction
HKL-3000
datascaling
BUSTER
2.8.0
refinement
Refinement
Method to determine structure: MAD / Resolution: 2.8→29.71 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.842 / Cross valid method: THROUGHOUT / σ(F): 0 Details: Model was refined against inflection wavelength data
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.289
430
4.77 %
RANDOM
Rwork
0.218
-
-
-
obs
0.221
9013
-
-
Displacement parameters
Biso mean: 29.79 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-3.702 Å2
0 Å2
0 Å2
2-
-
7.505 Å2
0 Å2
3-
-
-
-3.803 Å2
Refine analyze
Luzzati coordinate error obs: 0.376 Å
Refinement step
Cycle: LAST / Resolution: 2.8→29.71 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2287
0
11
0
2298
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2326
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.12
3157
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
785
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
54
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
348
HARMONIC
5
X-RAY DIFFRACTION
t_it
2326
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.72
X-RAY DIFFRACTION
t_other_torsion
19.9
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
305
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
2621
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→3.13 Å / Total num. of bins used: 5
Rfactor
Num. reflection
% reflection
Rfree
0.354
142
5.69 %
Rwork
0.228
2355
-
all
0.235
2497
-
+
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