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Crystal structure of avidin complex with a ferrocene biotin derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292.15 0.2M potassium thiocyanate, 0.1M BIS-TRIS pH 6.5 and 22% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.2 α = 90 b = 74.91 β = 106.17 c = 76.18 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 100 PIXEL DECTRIS PILATUS 6M 2013-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.07106 PETRA III, EMBL c/o DESY P13 (MX1)
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 50 91.8 0.048 12.57 2.93 14959
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 3VGW 2.5 37.46 14210 749 91.94 0.20444 0.2018 0.2072 0.25354 0.2519 RANDOM 65.478
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] -4.23 -5.3 1.62 4.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.971 r_dihedral_angle_3_deg 18.81 r_dihedral_angle_4_deg 14.159 r_dihedral_angle_1_deg 7.637 r_long_range_B_refined 6.85 r_long_range_B_other 6.849 r_scangle_other 3.35 r_mcangle_it 3.058 r_mcangle_other 3.058 r_scbond_it 2.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.971 r_dihedral_angle_3_deg 18.81 r_dihedral_angle_4_deg 14.159 r_dihedral_angle_1_deg 7.637 r_long_range_B_refined 6.85 r_long_range_B_other 6.849 r_scangle_other 3.35 r_mcangle_it 3.058 r_mcangle_other 3.058 r_scbond_it 2.663 r_scbond_other 2.663 r_angle_refined_deg 2.026 r_angle_other_deg 1.792 r_mcbond_it 1.784 r_mcbond_other 1.784 r_chiral_restr 0.111 r_bond_refined_d 0.018 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.01 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3620 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing