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Structure of apo Bradavidin2 (Form B)
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 3 293 1 uL drop of 3.4 mg/mL protein in 0.5 M acetic acid, pH 3.0, with 0.12 M magnesium formate, diffraction parameters improved with later addition of 0.1 M sodium bromide, MICROBATCH, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.48 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.771 α = 106.59 b = 46.118 β = 106.92 c = 46.449 γ = 106.82
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 2011-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.98 ESRF ID29
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 1.693 50 86 23010 23010
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 1.693 40.66 21850 21850 1159 85.42 0.21473 0.21229 0.2114 0.25972 0.2602 RANDOM 26.69
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] 0.6 -0.16 -1.48 -1.02 -1.22 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.351 r_dihedral_angle_4_deg 22.716 r_dihedral_angle_3_deg 18.539 r_dihedral_angle_1_deg 7.177 r_scangle_it 3.94 r_scbond_it 2.721 r_mcangle_it 1.853 r_angle_refined_deg 1.677 r_mcbond_it 1.073 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.351 r_dihedral_angle_4_deg 22.716 r_dihedral_angle_3_deg 18.539 r_dihedral_angle_1_deg 7.177 r_scangle_it 3.94 r_scbond_it 2.721 r_mcangle_it 1.853 r_angle_refined_deg 1.677 r_mcbond_it 1.073 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.301 r_nbd_refined 0.244 r_symmetry_hbond_refined 0.224 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.147 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 1644 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling