DNA BINDING PROTEIN / RAG1 / V(D)J RECOMBINATION / ANTIBODY / MAD / RING FINGER / ZINC BINUCLEAR CLUSTER / ZINC FINGER / DNA-BINDING PROTEIN
Function / homology
Function and homology information
DNA recombinase complex / endodeoxyribonuclease complex / double-stranded DNA endonuclease activity / pre-B cell allelic exclusion / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / negative regulation of thymocyte apoptotic process / positive regulation of T cell differentiation / regulation of T cell differentiation ...DNA recombinase complex / endodeoxyribonuclease complex / double-stranded DNA endonuclease activity / pre-B cell allelic exclusion / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / negative regulation of thymocyte apoptotic process / positive regulation of T cell differentiation / regulation of T cell differentiation / T cell homeostasis / protein autoubiquitination / B cell differentiation / thymus development / RING-type E3 ubiquitin transferase / visual learning / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / chromatin organization / histone binding / T cell differentiation in thymus / endonuclease activity / DNA recombination / adaptive immune response / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function
Resolution: 2.1→20 Å / Num. obs: 36957 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24
Reflection shell
Resolution: 2.1→2.15 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.61 / % possible all: 95.6
Reflection shell
*PLUS
% possible obs: 95.6 %
-
Processing
Software
Name
Version
Classification
BAZFAZ
modelbuilding
X-PLOR
3.851
refinement
DENZO
datareduction
SCALEPACK
datascaling
BAZFAZ
phasing
Refinement
Method to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 4 Details: LOCAL SCALING USING MAXSCALE WAS USED TO CORRECT THE HIGHLY ANISOTROPIC DATA. THE LOW OVERALL COMPLETION OF THE DATA REFLECT THIS ANISOTROPY.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.257
668
9.6 %
RANDOM
Rwork
0.209
-
-
-
obs
0.209
6970
60.5 %
-
Displacement parameters
Biso mean: 28.7 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.3 Å
0.25 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.25 Å
0.21 Å
Refinement step
Cycle: LAST / Resolution: 2.1→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
911
0
4
52
967
Refine LS restraints
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_bond_d
0.01
X-RAY DIFFRACTION
x_bond_d_na
X-RAY DIFFRACTION
x_bond_d_prot
X-RAY DIFFRACTION
x_angle_d
X-RAY DIFFRACTION
x_angle_d_na
X-RAY DIFFRACTION
x_angle_d_prot
X-RAY DIFFRACTION
x_angle_deg
2.1
X-RAY DIFFRACTION
x_angle_deg_na
X-RAY DIFFRACTION
x_angle_deg_prot
X-RAY DIFFRACTION
x_dihedral_angle_d
24.2
X-RAY DIFFRACTION
x_dihedral_angle_d_na
X-RAY DIFFRACTION
x_dihedral_angle_d_prot
X-RAY DIFFRACTION
x_improper_angle_d
1.47
X-RAY DIFFRACTION
x_improper_angle_d_na
X-RAY DIFFRACTION
x_improper_angle_d_prot
X-RAY DIFFRACTION
x_mcbond_it
X-RAY DIFFRACTION
x_mcangle_it
X-RAY DIFFRACTION
x_scbond_it
X-RAY DIFFRACTION
x_scangle_it
LS refinement shell
Resolution: 2.1→2.2 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
Rfactor
Num. reflection
% reflection
Rfree
0.276
43
10.4 %
Rwork
0.259
372
-
obs
-
-
29.4 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
PARHCSDX.PRO
TOPHCSDX.PRO
X-RAY DIFFRACTION
2
PAR.WAT
TOP_116_117.ZN
X-RAY DIFFRACTION
3
PAR.ZN
TOP_118.ZN
X-RAY DIFFRACTION
4
TOP_119.ZN
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-ID
Type
Dev ideal
X-RAY DIFFRACTION
x_dihedral_angle_d
X-RAY DIFFRACTION
x_dihedral_angle_deg
24.2
X-RAY DIFFRACTION
x_improper_angle_d
X-RAY DIFFRACTION
x_improper_angle_deg
1.47
+
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