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Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IJ8 PDB entry 1ij8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 290 0.2M ammonium sulphate, 0.1M Na Cacodylate pH6.5, 30% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.1 40.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.584 α = 90 b = 79.052 β = 90 c = 42.997 γ = 90
Symmetry Space Group P 21 21 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 2004-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.9795 SRS PX14.2
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 52.7 97 0.102 0.102 18.2 8.1 8807 8538 2 2 39.5
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) Redundancy Number Unique Reflections (All) 1 2.5 2.59 95.9 95.9 0.71 0.71 2.3 8.3 822
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1ij8 2.5 52.7 2 8538 8515 400 96.92 0.225 0.225 0.221 0.2239 0.308 0.2949 RANDOM 39.447
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] 2 -0.4 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.708 r_dihedral_angle_4_deg 22.468 r_dihedral_angle_3_deg 18.794 r_dihedral_angle_1_deg 8.67 r_scangle_it 3.326 r_angle_refined_deg 2.17 r_scbond_it 1.969 r_mcangle_it 1.793 r_mcbond_it 1.054 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.708 r_dihedral_angle_4_deg 22.468 r_dihedral_angle_3_deg 18.794 r_dihedral_angle_1_deg 8.67 r_scangle_it 3.326 r_angle_refined_deg 2.17 r_scbond_it 1.969 r_mcangle_it 1.793 r_mcbond_it 1.054 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.145 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1924 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 66
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction