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Crystal structure of avidin - HABA complex (hexagonal crystal form)
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 292.15 0.1M sodium citrate tribasic dehydrate pH 4.5, 24% w/v polyethylene glycol 1000
Crystal Properties Matthews coefficient Solvent content 2.28 46.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.31 α = 90 b = 61.31 β = 90 c = 120.53 γ = 120
Symmetry Space Group P 64 2 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 PIXEL DECTRIS PILATUS 6M 2014-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.977609 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 50 100 31.92 5.1 7329
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 1VYO 2.2 40.18 6957 368 99.96 0.16401 0.1607 0.1734 0.22746 0.2339 RANDOM 72.69
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] -2.03 -1.02 -2.03 6.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_dihedral_angle_4_deg 25.006 r_dihedral_angle_3_deg 16.188 r_long_range_B_refined 11.323 r_long_range_B_other 11.318 r_dihedral_angle_1_deg 8.359 r_scangle_other 6.858 r_mcangle_it 6.491 r_mcangle_other 6.491 r_scbond_it 4.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.054 r_dihedral_angle_4_deg 25.006 r_dihedral_angle_3_deg 16.188 r_long_range_B_refined 11.323 r_long_range_B_other 11.318 r_dihedral_angle_1_deg 8.359 r_scangle_other 6.858 r_mcangle_it 6.491 r_mcangle_other 6.491 r_scbond_it 4.223 r_scbond_other 4.219 r_mcbond_it 3.819 r_mcbond_other 3.802 r_angle_refined_deg 2.003 r_angle_other_deg 1.134 r_chiral_restr 0.115 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 946 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing