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Crystal structure of core-bradavidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y32 PDB ENTRY 2Y32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP ONE MICROLITER OF THE PROTEIN SOLUTION (LESS THAN 1 MG PER ML AND IN 50 MM SODIUM ACETATE, 100 MM NACL, PH 4) WAS CRYSTALLIZED BY ADDING ONE MICROLITER OF THE WELL SOLUTION (0.1 M HEPES PH 7.4, 0.8 M K,NA TARTRATE).HANGING DROPS AND VAPOUR DIFFUSION METHOD WAS USED AT RT. BEFORE CRYSTALLIZATION, 25 MICROLITERS OF THE PROTEIN SAMPLE WAS INCUBATED WITH 1 MICRO LITER OF BIOTIN SOLUTION (1 MG PER ML AND IN 5 MM TRIS PH 8.8, 8 MM CHES PH 9.5) FOR 3.5 HOURS AT 37 DEGREES OF CELCIUS.
Crystal Properties Matthews coefficient Solvent content 2 38.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.946 α = 90 b = 78.647 β = 90 c = 100.12 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 2005-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 1.6 25 100 0.09 18 9.6 52798 -3
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 1.6 1.7 100 0.55 4 9.6
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 PDB ENTRY 2Y32 1.6 61.9 50108 2690 99.95 0.14843 0.14685 0.173 0.17863 0.2013 RANDOM 14.577
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] 1.11 -0.78 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_3_deg 10.92 r_dihedral_angle_1_deg 6.071 r_scangle_it 2.715 r_scbond_it 1.838 r_angle_refined_deg 1.457 r_mcangle_it 1.224 r_mcbond_it 0.626 r_chiral_restr 0.099 r_bond_refined_d 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.969 r_dihedral_angle_3_deg 10.92 r_dihedral_angle_1_deg 6.071 r_scangle_it 2.715 r_scbond_it 1.838 r_angle_refined_deg 1.457 r_mcangle_it 1.224 r_mcbond_it 0.626 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other 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_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 3313 Nucleic Acid Atoms Solvent Atoms 368 Heterogen Atoms 82
Software Software Software Name Purpose REFMAC refinement XDS data reduction PHASER phasing