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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 PDB ENTRY 1YUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 0.2M Magnesium acetate, 0.1M sodium acetate, pH4.6, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.89 34.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.489 α = 90 b = 30.853 β = 94.29 c = 65.157 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 2006-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 1.75 27.87 21822
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 PDB ENTRY 1YUK 1.75 27.87 21815 1117 91.34 0.207 0.204 0.1983 0.253 0.248 RANDOM 20.372
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] -0.21 0.2 -0.02 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.744 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_4_deg 12.783 r_dihedral_angle_1_deg 5.817 r_scangle_it 1.794 r_angle_refined_deg 1.169 r_scbond_it 1.101 r_mcangle_it 0.649 r_mcbond_it 0.378 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.744 r_dihedral_angle_3_deg 15.033 r_dihedral_angle_4_deg 12.783 r_dihedral_angle_1_deg 5.817 r_scangle_it 1.794 r_angle_refined_deg 1.169 r_scbond_it 1.101 r_mcangle_it 0.649 r_mcbond_it 0.378 r_nbtor_refined 0.301 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.133 r_xyhbond_nbd_refined 0.111 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2156 Nucleic Acid Atoms Solvent Atoms 268 Heterogen Atoms 42
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction SCALA data scaling