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Crystal structure of avidin - biotinylruthenocene complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 35% pentaerythritol propoxylate, 0.05M HEPES, 0.2M KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 1.98 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.22 α = 90 b = 60.22 β = 90 c = 62.47 γ = 90
Symmetry Space Group P 42 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 2011-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8015 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 43.36 99.8 0.132 19.49 9.07 4308 4301 -3 30.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 99.6 0.505 4.75 8.59 458
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1VYO 2.5 43.3 4308 4085 216 99.84 0.16711 0.16711 0.16469 0.1657 0.21103 0.2116 RANDOM 34.055
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.372 r_dihedral_angle_4_deg 24.83 r_dihedral_angle_3_deg 19.808 r_dihedral_angle_1_deg 7.868 r_angle_refined_deg 2.264 r_chiral_restr 0.122 r_gen_planes_refined 0.039 r_bond_refined_d 0.018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1006 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling