2JCP

The hyaluronan binding domain of murine CD44


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UUHPDB ENTRY 1UUH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5DROPLETS COMPRISING 200NL CD4425-174 (AT A CONCENTRATION OF 0.5MM) MIXED WITH 200NL WELL SOLUTION WERE DISPENSED AS SITTING DROPS AND UNDERWENT VAPOR DIFFUSION WITH A WELL SOLUTION OF 30% PEG MONOMETHYLETHER 5000, AND 200 MM (NH4)2SO4 IN 100 MM MES BUFFER PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.726α = 90
b = 82.097β = 117.92
c = 32.336γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.341.0599.50.066.42.634562
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)
11.31.3799.20.23.22.6

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 1UUH1.341.1732795173699.40.1580.1570.191RANDOM11.82
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]
-0.1-0.10.03-0.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_4_deg19.975
r_dihedral_angle_3_deg10.802
r_dihedral_angle_1_deg6.818
r_scangle_it3.305
r_scbond_it2.405
r_mcangle_it1.603
r_angle_refined_deg1.262
r_mcbond_it1.04
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.02
r_dihedral_angle_4_deg19.975
r_dihedral_angle_3_deg10.802
r_dihedral_angle_1_deg6.818
r_scangle_it3.305
r_scbond_it2.405
r_mcangle_it1.603
r_angle_refined_deg1.262
r_mcbond_it1.04
r_nbtor_refined0.313
r_xyhbond_nbd_refined0.274
r_symmetry_vdw_refined0.197
r_nbd_refined0.196
r_symmetry_hbond_refined0.086
r_chiral_restr0.081
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing