- PDB-5nir: Crystal structure of collagen 2A vWC domain -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5nir
Title
Crystal structure of collagen 2A vWC domain
Components
Collagen alpha-1(II) chain
Keywords
STRUCTURAL PROTEIN / collagen / vwc / ECM / BMP-2
Function / homology
Function and homology information
collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / platelet-derived growth factor binding / Extracellular matrix organization / notochord development / limb bud formation / cartilage development involved in endochondral bone morphogenesis / extracellular matrix structural constituent conferring tensile strength / Collagen biosynthesis and modifying enzymes / tissue homeostasis / MHC class II protein binding / cellular response to BMP stimulus / Signaling by PDGF / endochondral ossification / NCAM1 interactions / collagen fibril organization / cartilage development / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / MET activates PTK2 signaling / cartilage condensation / inner ear morphogenesis / roof of mouth development / Collagen degradation / Non-integrin membrane-ECM interactions / basement membrane / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / extrinsic apoptotic signaling pathway in absence of ligand / visual perception / skeletal system development / central nervous system development / sensory perception of sound / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of gene expression / collagen-containing extracellular matrix / endoplasmic reticulum lumen / protein homodimerization activity / extracellular space / extracellular region / metal ion binding Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.96861 Å / Relative weight: 1
Reflection
Resolution: 1.74→49.37 Å / Num. obs: 17667 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.54 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 22.7
Reflection shell
Resolution: 1.744→1.75 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.709 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.709 / % possible all: 100
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Processing
Software
Name
Version
Classification
AutoPROC
datareduction
XDS
(VERSIONSeptember2
datareduction
Aimless
datascaling
BUSTER
2.10.3
refinement
autoSHARP
phasing
SCALA
datascaling
Refinement
Method to determine structure: SAD / Resolution: 1.74→49.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.115 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.106
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.231
894
5.07 %
RANDOM
Rwork
0.209
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-
-
obs
0.21
17616
99.2 %
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Displacement parameters
Biso mean: 39.26 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-5.5435 Å2
0 Å2
0 Å2
2-
-
2.6156 Å2
0 Å2
3-
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2.9278 Å2
Refine analyze
Luzzati coordinate error obs: 0.26 Å
Refinement step
Cycle: LAST / Resolution: 1.74→49.37 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
993
0
181
16
1190
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
Restraint function
Weight
X-RAY DIFFRACTION
t_bond_d
0.01
1223
HARMONIC
2
X-RAY DIFFRACTION
t_angle_deg
1.22
1591
HARMONIC
2
X-RAY DIFFRACTION
t_dihedral_angle_d
478
SINUSOIDAL
2
X-RAY DIFFRACTION
t_incorr_chiral_ct
X-RAY DIFFRACTION
t_pseud_angle
X-RAY DIFFRACTION
t_trig_c_planes
33
HARMONIC
2
X-RAY DIFFRACTION
t_gen_planes
147
HARMONIC
5
X-RAY DIFFRACTION
t_it
1223
HARMONIC
20
X-RAY DIFFRACTION
t_nbd
X-RAY DIFFRACTION
t_omega_torsion
3.94
X-RAY DIFFRACTION
t_other_torsion
14.98
X-RAY DIFFRACTION
t_improper_torsion
X-RAY DIFFRACTION
t_chiral_improper_torsion
147
SEMIHARMONIC
5
X-RAY DIFFRACTION
t_sum_occupancies
X-RAY DIFFRACTION
t_utility_distance
X-RAY DIFFRACTION
t_utility_angle
X-RAY DIFFRACTION
t_utility_torsion
X-RAY DIFFRACTION
t_ideal_dist_contact
1435
SEMIHARMONIC
4
LS refinement shell
Resolution: 1.74→1.84 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
Rfactor
Num. reflection
% reflection
Rfree
0.257
140
5.22 %
Rwork
0.222
2540
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all
0.224
2680
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obs
-
-
95.15 %
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