2OZ4

Structural Plasticity in IgSF Domain 4 of ICAM-1 Mediates Cell Surface Dimerization


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.5M LITHIUM SULFATE, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4964.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 185.396α = 90
b = 69.342β = 112.76
c = 88.173γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97949APS19-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
12.73090.60.0870.08711.13.52601526015
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)
12.72.858.10.5430.5431.22.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 entries 1F11, 1P532.728.5259592340025591000.2090.2040.253RANDOM63.34
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]
-5.52-4.126.95-4.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.831
r_dihedral_angle_4_deg12.788
r_dihedral_angle_3_deg10.599
r_dihedral_angle_1_deg4.96
r_angle_refined_deg0.903
r_mcangle_it0.897
r_scangle_it0.865
r_angle_other_deg0.656
r_mcbond_it0.627
r_scbond_it0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.831
r_dihedral_angle_4_deg12.788
r_dihedral_angle_3_deg10.599
r_dihedral_angle_1_deg4.96
r_angle_refined_deg0.903
r_mcangle_it0.897
r_scangle_it0.865
r_angle_other_deg0.656
r_mcbond_it0.627
r_scbond_it0.49
r_nbd_other0.164
r_nbtor_refined0.163
r_symmetry_vdw_other0.153
r_nbd_refined0.149
r_symmetry_vdw_refined0.093
r_chiral_restr0.091
r_xyhbond_nbd_refined0.091
r_metal_ion_refined0.09
r_symmetry_hbond_refined0.088
r_nbtor_other0.077
r_symmetry_metal_ion_refined0.066
r_mcbond_other0.016
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5234
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing