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Structure of the PHE2 and PHE3 fragments of the integrin beta2 subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YUK 1YUK, 1L3Y experimental model PDB 1L3Y 1YUK, 1L3Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2M ammonium sulphate, 15% PEG4000, 5% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.26 α = 90 b = 52.26 β = 90 c = 423.924 γ = 120
Symmetry Space Group P 65 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2006-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 25 18866
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.257
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1YUK, 1L3Y 2.2 25 18723 964 99.29 0.263 0.261 0.3088 0.308 0.3433 RANDOM 22.65
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] 0.16 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.312 r_scangle_it 2.281 r_mcangle_it 1.337 r_scbond_it 1.332 r_angle_refined_deg 1.223 r_angle_other_deg 0.8 r_mcbond_it 0.716 r_symmetry_vdw_other 0.231 r_nbd_other 0.221 r_symmetry_vdw_refined 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.312 r_scangle_it 2.281 r_mcangle_it 1.337 r_scbond_it 1.332 r_angle_refined_deg 1.223 r_angle_other_deg 0.8 r_mcbond_it 0.716 r_symmetry_vdw_other 0.231 r_nbd_other 0.221 r_symmetry_vdw_refined 0.185 r_nbd_refined 0.174 r_xyhbond_nbd_refined 0.174 r_symmetry_hbond_refined 0.158 r_nbtor_other 0.081 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2355 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 15
Software Software Software Name Purpose AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASES phasing