Mass: 24919.762 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F) (reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J),All residures includes ...Details: All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F) (reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J),All residures includes purification tag of A3F(6His+thrombin cleavage tag+ chimeric A3F)(reference: K. Siu, et al. Nat. Commun. 2013, 4, 2593. PDB code:4J4J) Source: (gene. exp.) Homo sapiens (human) / Gene: APOBEC3G, MDS019, APOBEC3F Production host: prokaryotic environmental samples (environmental samples) References: UniProt: Q9HC16, UniProt: Q8IUX4, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In cyclic amidines
Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 3, 2017
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.9793 Å / Relative weight: 1
Reflection
Resolution: 2.3→45.68 Å / Num. obs: 23245 / % possible obs: 98.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 14
Reflection shell
Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.619
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
PHENIX
1.9_1692
refinement
HKL-2000
datascaling
PHASES
phasing
PDB_EXTRACT
3.24
dataextraction
ADDREF
datareduction
Refinement
Method to determine structure: SAD / Resolution: 2.3→45.68 Å / SU B: 12.618 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.193 / Details: U VALUES : WITH TLS ADDED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.208
1158
5 %
RANDOM
Rwork
0.161
-
-
-
obs
0.164
21994
98.7 %
-
Displacement parameters
Biso mean: 50.96 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-2.71 Å2
0 Å2
0 Å2
2-
-
2.18 Å2
0 Å2
3-
-
-
0.53 Å2
Refinement step
Cycle: LAST / Resolution: 2.3→45.68 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
3106
178
16
115
3415
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
0.0768
0.0152
-0.0574
0.1379
-0.0488
0.054
0.0052
-0.0045
0.0073
0.0048
-0.007
-0.0087
-0.0018
0.005
0.0018
0.0739
0.0001
-0.0052
0.0009
-0.0007
0.039
-22.3506
-5.428
-4.0854
2
0.035
-0.0547
0.0039
0.0862
-0.0158
0.169
-0.0037
-0.0033
-0.0017
0.0041
0.0057
-0.0002
0.0025
-0.0016
-0.002
0.0714
-0.0009
0.0003
0.0005
-0.0021
0.0385
-8.2109
-28.4956
28.923
3
6.5691
0.58
2.2116
0.2317
-0.2378
1.7847
0.0359
0.0257
-0.3485
-0.1495
-0.0081
-0.0676
0.3715
0.042
-0.0277
0.1752
-0.0354
0.0297
0.0457
-0.0023
0.0367
-30.9308
-26.9196
12.6758
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid -32 through 373 )
2
X-RAY DIFFRACTION
2
chain 'B' and (resid -29 through 373 )
3
X-RAY DIFFRACTION
3
chain 'C' and (resid1through10 )
+
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