- PDB-4x1j: X-ray crystal structure of the dimeric BMP antagonist NBL1 -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4x1j
Title
X-ray crystal structure of the dimeric BMP antagonist NBL1
Components
Neuroblastoma suppressor of tumorigenicity 1
Keywords
BMP Binding Protein / BMP antagonist / DAN family / Cystine-knot
Function / homology
Function and homology information
sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity / morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / animal organ morphogenesis ...sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity / morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / animal organ morphogenesis / nervous system development / receptor ligand activity / extracellular space / identical protein binding Similarity search - Function
Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 7, 2013
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.979 Å / Relative weight: 1
Reflection
Resolution: 2.5→55.18 Å / Num. obs: 9690 / % possible obs: 99.68 % / Redundancy: 12.3 % / Net I/σ(I): 23.5
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
XDS
datareduction
Aimless
datascaling
PHASER
phasing
Refinement
Resolution: 2.5→55.18 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.914 / SU B: 21.712 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.27315
964
10 %
RANDOM
Rwork
0.21576
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obs
0.22175
8674
99.68 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK