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Crystal structure of chimeric avidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AVI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.3 293 20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 46.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.657 α = 90 b = 124.791 β = 114.45 c = 88.895 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 315r 2008-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.98 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 94.42 98.1 0.076 14.3 3.7 42677 42677
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) 2.7 2.75 90.1 0.63 0.63 1.3 3.3
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 (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 2AVI 2.7 50 40310 40311 2141 98.01 0.22592 0.2218 0.2299 0.30929 0.3173 RANDOM 48.114
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] -1.99 -1.01 5.23 -4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.182 r_dihedral_angle_3_deg 22.69 r_dihedral_angle_4_deg 21.065 r_dihedral_angle_1_deg 7.715 r_scangle_it 2.417 r_angle_refined_deg 1.79 r_scbond_it 1.467 r_mcangle_it 1.158 r_mcbond_it 0.626 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.182 r_dihedral_angle_3_deg 22.69 r_dihedral_angle_4_deg 21.065 r_dihedral_angle_1_deg 7.715 r_scangle_it 2.417 r_angle_refined_deg 1.79 r_scbond_it 1.467 r_mcangle_it 1.158 r_mcbond_it 0.626 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.265 r_symmetry_hbond_refined 0.212 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10923 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling