5BZC

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
2.1542.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.97α = 90
b = 81.94β = 117.91
c = 32.06γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-12012-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.000ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.9440.97970.0980.11414.3710233-317.864
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.941.9988.20.3820.4483.43

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 REPLACEMENTTHROUGHOUT1.9540.97961853097.790.18410.18160.2317RANDOM11.037
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]
-0.19-0.330.57-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.144
r_dihedral_angle_4_deg19.027
r_dihedral_angle_3_deg11.779
r_dihedral_angle_1_deg6.811
r_scangle_it3.528
r_scbond_it2.185
r_angle_refined_deg1.466
r_mcangle_it1.259
r_mcbond_it0.72
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.144
r_dihedral_angle_4_deg19.027
r_dihedral_angle_3_deg11.779
r_dihedral_angle_1_deg6.811
r_scangle_it3.528
r_scbond_it2.185
r_angle_refined_deg1.466
r_mcangle_it1.259
r_mcbond_it0.72
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1171
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction