4MRF

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
2.1442.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.805α = 90
b = 81.626β = 118.28
c = 32.358γ = 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
11.5540.898.80.0310.04222.13.2203122019221.5
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)
11.551.6395.50.0850.0858.82.52840

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 2JCP1.5540.820133102898.750.18190.18010.215RANDOM13.8573
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]
-0.67-0.550.46-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_4_deg17.972
r_dihedral_angle_3_deg11.87
r_dihedral_angle_1_deg7.02
r_scangle_it4.373
r_scbond_it2.711
r_mcangle_it1.727
r_angle_refined_deg1.523
r_mcbond_it1.014
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.266
r_dihedral_angle_4_deg17.972
r_dihedral_angle_3_deg11.87
r_dihedral_angle_1_deg7.02
r_scangle_it4.373
r_scbond_it2.711
r_mcangle_it1.727
r_angle_refined_deg1.523
r_mcbond_it1.014
r_chiral_restr0.109
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1171
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms25

Software

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