2P28

Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YUK1YUK, 1L3Y
experimental modelPDB 1L3Y1YUK, 1L3Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.2M ammonium sulphate, 15% PEG4000, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3948.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.26α = 90
b = 52.26β = 90
c = 423.924γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-09-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.976ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.22518866
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.257

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 REPLACEMENTTHROUGHOUT1YUK, 1L3Y2.2251872396499.290.2630.2610.308RANDOM22.65
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]
0.160.080.16-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.312
r_scangle_it2.281
r_mcangle_it1.337
r_scbond_it1.332
r_angle_refined_deg1.223
r_angle_other_deg0.8
r_mcbond_it0.716
r_symmetry_vdw_other0.231
r_nbd_other0.221
r_symmetry_vdw_refined0.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.312
r_scangle_it2.281
r_mcangle_it1.337
r_scbond_it1.332
r_angle_refined_deg1.223
r_angle_other_deg0.8
r_mcbond_it0.716
r_symmetry_vdw_other0.231
r_nbd_other0.221
r_symmetry_vdw_refined0.185
r_nbd_refined0.174
r_xyhbond_nbd_refined0.174
r_symmetry_hbond_refined0.158
r_nbtor_other0.081
r_chiral_restr0.071
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2355
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms15

Software

Software
Software NamePurpose
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing