2WUH

Crystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QQJPDB ENTRIES 2QQJ AND 2V53
experimental modelPDB 2V53PDB ENTRIES 2QQJ AND 2V53

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.140.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.397α = 66.19
b = 40.863β = 88.9
c = 48.917γ = 76.92
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2008-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.62090.20.0516.83.827359
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6967.40.284.33.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRIES 2QQJ AND 2V531.62027359272690.30.20190.20190.2298RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.3826.95-2.3510.993-4.021-2.375
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.49
c_mcangle_it2.02
c_scbond_it1.96
c_angle_deg1.5
c_mcbond_it1.3
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
RMS Deviations
KeyRefinement Restraint Deviation
c_scangle_it2.49
c_mcangle_it2.02
c_scbond_it1.96
c_angle_deg1.5
c_mcbond_it1.3
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1845
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms

Software

Software
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing