Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
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Details
Has protein modification
Y
Sequence details
N-TERMINAL DOMAIN OF HUMAN RGMB WITH 3 ADDITIONAL N- TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C- ...N-TERMINAL DOMAIN OF HUMAN RGMB WITH 3 ADDITIONAL N- TERMINAL RESIDUES (ETG) AND 9 ADDITIONAL C-TERMINAL RESIDUES (GTKHHHHHH).
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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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9173 Å / Relative weight: 1
Reflection
Resolution: 2.8→45 Å / Num. obs: 13647 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 69.81 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.7
Reflection shell
Resolution: 2.8→2.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.7 / % possible all: 99.4
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Processing
Software
Name
Version
Classification
BUSTER
2.10.2
refinement
XDS
datareduction
SCALA
datascaling
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45 Å / Cor.coef. Fo:Fc: 0.8968 / Cor.coef. Fo:Fc free: 0.9102 / SU R Cruickshank DPI: 0.462 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.473 / SU Rfree Blow DPI: 0.303 / SU Rfree Cruickshank DPI: 0.304 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2665
588
4.79 %
RANDOM
Rwork
0.2327
-
-
-
obs
0.2344
12284
99.85 %
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Displacement parameters
Biso mean: 87.99 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-12.7622 Å2
0 Å2
0 Å2
2-
-
-12.7622 Å2
0 Å2
3-
-
-
25.5243 Å2
Refine analyze
Luzzati coordinate error obs: 0.546 Å
Refinement step
Cycle: LAST / Resolution: 2.8→45 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2018
0
22
20
2060
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2094
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.08
2854
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
939
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
49
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
301
HARMONIC
5
X-RAY DIFFRACTION
t_it
2094
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.11
X-RAY DIFFRACTION
t_other_torsion
3.05
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
269
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
2371
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.8→3.07 Å / Total num. of bins used: 6
Rfactor
Num. reflection
% reflection
Rfree
0.4208
142
4.92 %
Rwork
0.3448
2742
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all
0.3482
2884
-
obs
-
-
99.85 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
2.6205
1.7185
-2.3156
1.1108
-1.1795
4.5005
0.0269
0.0142
0.1531
-0.0499
0.0495
0.1648
-0.2026
-0.1697
-0.0764
-0.0066
0.1363
0.0108
-0.0095
-0.0417
-0.2125
35.9843
-34.3494
23.2569
2
3.7149
2.1684
-3.676
2.9764
-3.4394
5.5895
-0.2133
-0.0076
0.1702
-0.1548
0.1403
0.1379
-0.1878
-0.2206
0.0729
0.1287
0.1186
-0.0202
-0.1312
-0.0676
-0.2962
45.6479
-26.5357
9.74
3
1.4332
-0.1409
-2.001
5.0517
4.9068
4.1167
-0.0873
0.3845
-0.0091
-0.3054
0.1865
0.145
0.2127
-0.0811
-0.0992
0.3187
0.0384
0.1913
0.0481
-0.1309
-0.3581
34.6028
-54.3969
12.3319
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
{ A|293 - A|396 }
2
X-RAY DIFFRACTION
2
{ B|293 - B|396 }
3
X-RAY DIFFRACTION
3
{ C|53 - C|121 }
+
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