4MRH

Crystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JCPpdb entry 2JCP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529830% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.987α = 90
b = 81.744β = 118.21
c = 32.236γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-11-17MSINGLE 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)R Sym 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
11.1281.7497.70.0360.04916.73.2531695286312.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.121.1894.70.1590.1594.537454

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 entry 2JCP1.1240.8752824270697.50.16990.16910.1838RANDOM11.8071
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]
-0.14-0.34-0.02-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.343
r_dihedral_angle_4_deg19.484
r_dihedral_angle_3_deg11.029
r_dihedral_angle_1_deg7.314
r_scangle_it3.812
r_scbond_it2.423
r_mcangle_it1.628
r_angle_refined_deg1.541
r_mcbond_it0.935
r_chiral_restr0.104
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.343
r_dihedral_angle_4_deg19.484
r_dihedral_angle_3_deg11.029
r_dihedral_angle_1_deg7.314
r_scangle_it3.812
r_scbond_it2.423
r_mcangle_it1.628
r_angle_refined_deg1.541
r_mcbond_it0.935
r_chiral_restr0.104
r_bond_refined_d0.014
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1171
Nucleic Acid Atoms
Solvent Atoms123
Heterogen Atoms14

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
XDSdata reduction