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Crystal structure of avidin in complex with 1-desthiobiotinylpyrene
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 6.5 292.15 Morpheus Screen (Molecular Dimensions) A1 solution (0.1 M IMIDAZOLE/MES MONOHYDRATE (ACID) BUFFER PH
6.5, 10% W/V POLYETHYLENE GLYCOL 20000, 20% V/V PEG 500 MME,
0.03 M MAGNESIUM CHLORIDE HEXAHYDRATE AND 0.03 M CALCIUM CHLORIDE DIHYDRATE), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K
Crystal Properties Matthews coefficient Solvent content 2.26 45.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.97 α = 90 b = 81.52 β = 90 c = 107.78 γ = 90
Symmetry Space Group P 21 21 21
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 2015-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.99999 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 2.1 50 99.9 0.041 24.34 6.53 30993
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 2.1 43.68 29440 1551 99.86 0.19721 0.19541 0.2015 0.23103 0.2318 RANDOM 67.376
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] -0.64 0.45 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.733 r_dihedral_angle_4_deg 23.744 r_dihedral_angle_3_deg 15.26 r_long_range_B_refined 7.808 r_long_range_B_other 7.808 r_dihedral_angle_1_deg 7.443 r_scangle_other 4.682 r_mcangle_it 3.722 r_mcangle_other 3.722 r_scbond_it 3.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.733 r_dihedral_angle_4_deg 23.744 r_dihedral_angle_3_deg 15.26 r_long_range_B_refined 7.808 r_long_range_B_other 7.808 r_dihedral_angle_1_deg 7.443 r_scangle_other 4.682 r_mcangle_it 3.722 r_mcangle_other 3.722 r_scbond_it 3.183 r_scbond_other 3.182 r_mcbond_it 2.507 r_mcbond_other 2.503 r_angle_refined_deg 1.956 r_angle_other_deg 1.954 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.011 r_gen_planes_other 0.009 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 3784 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 151
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing