2JCQ

The hyaluronan binding domain of murine CD44 in a Type A complex with an HA 8-mer


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT EITHER PH 7.0 OR PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.794α = 90
b = 82.051β = 117.89
c = 32.278γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.2523.4292.70.076.755.4436225
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)
11.251.3256.20.421.772.65

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 1UUH1.2541.0336568194598.40.1320.130.156RANDOM7.6
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]
0.04-0.26-0.15-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.887
r_dihedral_angle_4_deg18.856
r_dihedral_angle_3_deg11.841
r_dihedral_angle_1_deg7.169
r_scangle_it4.064
r_scbond_it3.2
r_mcangle_it2.129
r_angle_refined_deg1.774
r_mcbond_it1.718
r_angle_other_deg0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.887
r_dihedral_angle_4_deg18.856
r_dihedral_angle_3_deg11.841
r_dihedral_angle_1_deg7.169
r_scangle_it4.064
r_scbond_it3.2
r_mcangle_it2.129
r_angle_refined_deg1.774
r_mcbond_it1.718
r_angle_other_deg0.86
r_symmetry_vdw_refined0.25
r_symmetry_vdw_other0.25
r_nbd_refined0.237
r_nbd_other0.195
r_nbtor_refined0.186
r_xyhbond_nbd_refined0.18
r_symmetry_hbond_refined0.154
r_chiral_restr0.101
r_nbtor_other0.085
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms1164
Nucleic Acid Atoms
Solvent Atoms175
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing