3BN3

crystal structure of ICAM-5 in complex with aL I domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T0PPDB IDS 1T0P AND 1IC1
experimental modelPDB 1IC1PDB IDS 1T0P AND 1IC1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52960.1M HEPES pH7.5, 7.5%PEG8000, 10%glycerol, 5mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
3.7366.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.793α = 90
b = 71.507β = 90
c = 143.871γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97931APS19-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
12.09971.9898.60.0720.0548.23730333.3
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)
12.0992.1895.50.4540.4713.765.63564

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 (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUTPDB IDS 1T0P AND 1IC12.09971.983730337303186398.030.1930.1930.1910.20.2350.24RANDOM43.703
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]
-0.714.05-3.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.189
r_dihedral_angle_4_deg13.636
r_dihedral_angle_3_deg13.285
r_dihedral_angle_1_deg5.929
r_scangle_it4.104
r_mcangle_it3.484
r_mcbond_it2.855
r_scbond_it2.709
r_angle_refined_deg1.32
r_angle_other_deg0.816
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3000
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms97

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing