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The structure of apo bradavidin2 (Form A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EW1 PDB ENTRY 3EW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 30% PEG4000, 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, MICROBATCH, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.099 α = 90 b = 46.061 β = 116.66 c = 47.18 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 210 2010-09-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93 ESRF ID14-4
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 1.9 50 96.4 9133 9133
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 PDB ENTRY 3EW1 1.9 42.17 8650 8650 437 95.66 0.23799 0.23594 0.2351 0.27489 0.2734 RANDOM 35.469
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] 1.64 -1.6 -1.8 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.243 r_dihedral_angle_3_deg 23.444 r_dihedral_angle_4_deg 21.91 r_dihedral_angle_1_deg 7.469 r_scangle_it 3.546 r_scbond_it 2.555 r_mcangle_it 1.977 r_angle_refined_deg 1.756 r_mcbond_it 1.125 r_symmetry_vdw_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.243 r_dihedral_angle_3_deg 23.444 r_dihedral_angle_4_deg 21.91 r_dihedral_angle_1_deg 7.469 r_scangle_it 3.546 r_scbond_it 2.555 r_mcangle_it 1.977 r_angle_refined_deg 1.756 r_mcbond_it 1.125 r_symmetry_vdw_refined 0.337 r_nbtor_refined 0.326 r_symmetry_hbond_refined 0.285 r_nbd_refined 0.254 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.127 r_bond_refined_d 0.014 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 826 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling