2JCR

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JCQPDB ENTRY 2JCQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18CO-CRYSTALS OF THE CD44/HA8 COMPLEX WERE PREPARED AFTER ADDITION OF HA8 (2MM FINAL CONCENTRATION) TO THE 0.5 MM PROTEIN SOLUTION FOLLOWED BY MIXING 1:1 WITH WELL SOLUTIONS CONTAINING 25% (W/V) PEG 3350 AND 100MM NACL IN 100MM HEPES BUFFERED AT PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.8α = 90
b = 82.1β = 118
c = 32.4γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBRUKERMIRRORS2005-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR

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
1228.692.30.1110.42.59641
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)
122.0567.50.243.61.5

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 2JCQ228.61811440788.50.1790.1750.254RANDOM9.88
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]
-0.97-0.880.78-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.989
r_dihedral_angle_4_deg16.704
r_dihedral_angle_3_deg14.059
r_dihedral_angle_1_deg6.667
r_sphericity_free3.04
r_scangle_it2.161
r_scbond_it1.382
r_angle_refined_deg1.28
r_sphericity_bonded0.923
r_angle_other_deg0.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.989
r_dihedral_angle_4_deg16.704
r_dihedral_angle_3_deg14.059
r_dihedral_angle_1_deg6.667
r_sphericity_free3.04
r_scangle_it2.161
r_scbond_it1.382
r_angle_refined_deg1.28
r_sphericity_bonded0.923
r_angle_other_deg0.855
r_mcangle_it0.755
r_rigid_bond_restr0.711
r_mcbond_it0.559
r_symmetry_vdw_other0.255
r_nbd_refined0.196
r_nbd_other0.195
r_symmetry_vdw_refined0.191
r_symmetry_hbond_refined0.184
r_nbtor_refined0.172
r_mcbond_other0.164
r_xyhbond_nbd_refined0.161
r_nbtor_other0.081
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1172
Nucleic Acid Atoms
Solvent Atoms134
Heterogen Atoms99

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUMdata reduction
SAINTdata reduction
SADABSdata scaling
XSCALEdata scaling
MOLREPphasing