- PDB-5oxz: Crystal Structure of NeqN/NeqC complex from Nanoarcheaum equitans... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 5oxz
Title
Crystal Structure of NeqN/NeqC complex from Nanoarcheaum equitans at 1.2A
Components
NEQ068
NEQ528
Keywords
SPLICING / Intein complex 1
Function / homology
Function and homology information
nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding Similarity search - Function
Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B ...Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / DNA polymerase family B, thumb domain / DNA polymerase family B / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily Similarity search - Domain/homology
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97929 Å / Relative weight: 1
Reflection
Resolution: 1.2→42.41 Å / Num. obs: 51160 / % possible obs: 99.9 % / Redundancy: 12.2 % / Net I/σ(I): 16.2
Reflection shell
Resolution: 1.2→1.26 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 4 / % possible all: 99.9
-
Processing
Software
Name
Version
Classification
REFMAC
5.8.0158
refinement
XDS
datareduction
XDS
datascaling
Arcimboldo
phasing
Refinement
Method to determine structure: AB INITIO PHASING / Resolution: 1.2→42.4 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.901 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.15628
2482
4.9 %
RANDOM
Rwork
0.13731
-
-
-
obs
0.13823
48536
99.92 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å