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Crystal structure of avidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AVD PDB ENTRY 1AVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 295 Equal volumes (1 ul) of protein (0.5 mg/ml) in 50 mM Na acetate (pH 4) + 20 mM NaCl and well solution of 0.1 M MES (pH 6.6) + 24% PEG 8000 + 0.2 M Mg acetate
Crystal Properties Matthews coefficient Solvent content 2.15 42.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.949 α = 90 b = 78.772 β = 90 c = 43.01 γ = 90
Symmetry Space Group P 21 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 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 1.48 20 99 0.073 10 4 41811
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 1.48 1.58 99 0.47 3 4
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1AVD 1.48 19.1 39720 2091 100 0.167 0.165 0.19 RANDOM 7.58
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] 1.13 -0.35 -0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.972 r_scangle_it 3.246 r_scbond_it 2.013 r_angle_refined_deg 1.483 r_mcangle_it 1.226 r_angle_other_deg 0.849 r_mcbond_it 0.7 r_symmetry_vdw_other 0.303 r_nbd_other 0.257 r_symmetry_vdw_refined 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.972 r_scangle_it 3.246 r_scbond_it 2.013 r_angle_refined_deg 1.483 r_mcangle_it 1.226 r_angle_other_deg 0.849 r_mcbond_it 0.7 r_symmetry_vdw_other 0.303 r_nbd_other 0.257 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.097 r_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1905 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling AMoRE phasing