5BZS

Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298PEG MME 5000, MES, (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.1442.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.987α = 90
b = 81.744β = 118.205
c = 32.236γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.000APS17-ID

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
11.49840.8195.20.1628.43.321524
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)
11.4981.50393.50.3733.3203

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.540.8120316107995.110.21230.21070.242RANDOM4.011
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]
0.04-0.120.31-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.046
r_dihedral_angle_4_deg17.646
r_dihedral_angle_3_deg12.925
r_dihedral_angle_1_deg7.069
r_scangle_it2.673
r_scbond_it1.813
r_angle_refined_deg1.558
r_mcangle_it0.742
r_mcbond_it0.398
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.046
r_dihedral_angle_4_deg17.646
r_dihedral_angle_3_deg12.925
r_dihedral_angle_1_deg7.069
r_scangle_it2.673
r_scbond_it1.813
r_angle_refined_deg1.558
r_mcangle_it0.742
r_mcbond_it0.398
r_chiral_restr0.1
r_bond_refined_d0.016
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1171
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms30

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction