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Structure of Avidin in complex with the ligand deoxyguanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JJ8 PDB entry 1JJ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 50mM Na Citrate, 20% PEG 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.1 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.307 α = 90 b = 79.454 β = 90 c = 43.005 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 MAR CCD 165 mm mirrors 2005-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.488 SRS PX10.1
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 1.99 52.63 92.5 0.103 0.125 17.4 4.7 28039 15790 2 2 41.2
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 2.07 92.5 54.5 0.202 0.203 1.8 1.6 916
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 1JJ8 1.99 52.63 2 15758 15758 797 92.07 0.22 0.232 0.218 0.212 0.268 0.2545 RANDOM 42.052
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] 2.11 -1.95 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 23.928 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 8.788 r_scangle_it 3.857 r_scbond_it 2.478 r_mcangle_it 2.228 r_angle_refined_deg 1.944 r_mcbond_it 1.395 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.477 r_dihedral_angle_4_deg 23.928 r_dihedral_angle_3_deg 16.328 r_dihedral_angle_1_deg 8.788 r_scangle_it 3.857 r_scbond_it 2.478 r_mcangle_it 2.228 r_angle_refined_deg 1.944 r_mcbond_it 1.395 r_nbtor_refined 0.307 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.189 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.154 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1892 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 47
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction