Mass: 34967.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE ELECTRON DENSITY QUALITY IN THE FOLLOWING LOOP REGIONS OF CHAIN A IS VERY POOR OR ABSENT: 53-59, 88-93, 116-117, 137-146, 150-151, 297-300, 306-311. Source: (gene. exp.) Homo sapiens (human) / Gene: IBA57, C1orf69 / Production host: Escherichia coli (E. coli) References: UniProt: Q5T440, Transferases; Transferring one-carbon groups
Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1.54 Å / Relative weight: 1
Reflection
Resolution: 2.3→56.84 Å / Num. obs: 14998 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 39.36 Å2 / Rmerge(I) obs: 0.19 / Rsym value: 0.19 / Net I/σ(I): 6.5
Reflection shell
Resolution: 2.3→2.36 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.87 / % possible all: 97.5
-
Processing
Software
Name
Version
Classification
XDS
datareduction
XSCALE
datascaling
SHELXD
phasing
BUSTER
2.10.3
refinement
Refinement
Method to determine structure: SAD / Resolution: 2.3→56.84 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.862 / SU R Cruickshank DPI: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.314 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.23
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.228
800
5.25 %
RANDOM
Rwork
0.206
-
-
-
obs
0.208
15231
100 %
-
Displacement parameters
Biso mean: 45.89 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-7.6876 Å2
1.9728 Å2
-6.7954 Å2
2-
-
7.0027 Å2
1.4189 Å2
3-
-
-
0.6849 Å2
Refine analyze
Luzzati coordinate error obs: 0.32 Å
Refinement step
Cycle: LAST / Resolution: 2.3→56.84 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2343
0
64
76
2483
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
2470
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.07
3377
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
802
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
X-RAY DIFFRACTION
t_gen_planes
461
HARMONIC
5
X-RAY DIFFRACTION
t_it
2470
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
2.82
X-RAY DIFFRACTION
t_other_torsion
18.58
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
298
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
2715
SEMIHARMONIC
4
LS refinement shell
Resolution: 2.3→2.32 Å / Total num. of bins used: 40
Rfactor
Num. reflection
% reflection
Rfree
0.2662
-
4.99 %
Rwork
0.2271
362
-
all
0.2291
381
-
obs
-
-
99.48 %
Refinement TLS params.
Method: refined / Origin x: 32.2415 Å / Origin y: 42.6241 Å / Origin z: 37.2518 Å
11
12
13
21
22
23
31
32
33
T
-0.1936 Å2
0.0098 Å2
-0.0053 Å2
-
-0.0944 Å2
0.0239 Å2
-
-
0.0044 Å2
L
2.1348 °2
0.4982 °2
-0.0618 °2
-
4.5474 °2
0.2388 °2
-
-
3.6761 °2
S
0.0379 Å °
0.0438 Å °
0.0376 Å °
-0.047 Å °
0.0303 Å °
0.1153 Å °
-0.1012 Å °
-0.0121 Å °
-0.0682 Å °
Refinement TLS group
Selection details: { A|17 - A|324 }
+
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