meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching ...meiotic DNA integrity checkpoint signaling / checkpoint clamp complex / meiotic recombination checkpoint signaling / double-stranded DNA 3'-5' DNA exonuclease activity / exodeoxyribonuclease III / DNA replication checkpoint signaling / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / mitotic DNA replication checkpoint signaling / mitotic intra-S DNA damage checkpoint signaling / embryo development ending in birth or egg hatching / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / Activation of ATR in response to replication stress / response to UV / substantia nigra development / 3'-5' exonuclease activity / telomere maintenance / DNA damage checkpoint signaling / cellular response to ionizing radiation / nucleotide-excision repair / regulation of protein phosphorylation / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / histone deacetylase binding / SH3 domain binding / intrinsic apoptotic signaling pathway in response to DNA damage / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / intracellular membrane-bounded organelle / DNA repair / DNA damage response / nucleolus / protein kinase binding / enzyme binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function
Resolution: 3.2→3.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 4.2 / Num. unique all: 1272 / % possible all: 99.5
-
Processing
Software
Name
Version
Classification
HKL-2000
datacollection
PHENIX
modelbuilding
REFMAC
5.2.0019
refinement
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SIRAS / Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.851 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.306
1262
9.8 %
RANDOM
Rwork
0.289
-
-
-
obs
0.291
11575
99.48 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 67.81 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-1.42 Å2
0 Å2
-0.34 Å2
2-
-
8.4 Å2
0 Å2
3-
-
-
-7.06 Å2
Refinement step
Cycle: LAST / Resolution: 3.2→15 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6325
0
0
0
6325
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
6439
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.728
1.971
8707
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
8.759
5
803
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
41.618
24.596
285
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
24.413
15
1166
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
20.002
15
35
X-RAY DIFFRACTION
r_chiral_restr
0.113
0.2
1013
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.02
4769
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
0.29
0.2
3470
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
0.319
0.2
4150
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.207
0.2
216
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
0.28
0.2
123
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.249
0.2
10
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
7.698
2
4022
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
10.507
3
6514
X-RAY DIFFRACTION
r_scbond_it
0.027
2
2417
X-RAY DIFFRACTION
r_scangle_it
0.035
3
2193
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3.2→3.279 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.389
103
-
Rwork
0.412
786
-
obs
-
-
99 %
+
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