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Crystal structure of short hoefavidin biotin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Streak seeding was applied with source crystals. Crystals appeared within 24 hours and grew to their maximal size within 2 weeks
Crystal Properties Matthews coefficient Solvent content 2.72 54.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.18 α = 90 b = 61.18 β = 90 c = 166.86 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 6M 2013-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97 ESRF ID29
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 1.66 50 99.8 0.045 19.9 6.9 38372
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 1.66 1.72 0.798
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Z27 1.66 50 36448 1924 99.81 0.18194 0.17955 0.23017 0.2333 RANDOM 33.531
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] -2.02 -2.02 4.05
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.702 r_dihedral_angle_2_deg 39.761 r_sphericity_bonded 26.693 r_dihedral_angle_3_deg 13.643 r_scangle_other 8.931 r_scbond_it 7.619 r_scbond_other 7.619 r_long_range_B_other 7.11 r_long_range_B_refined 7.105 r_dihedral_angle_1_deg 6.996
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 42.702 r_dihedral_angle_2_deg 39.761 r_sphericity_bonded 26.693 r_dihedral_angle_3_deg 13.643 r_scangle_other 8.931 r_scbond_it 7.619 r_scbond_other 7.619 r_long_range_B_other 7.11 r_long_range_B_refined 7.105 r_dihedral_angle_1_deg 6.996 r_mcangle_other 6.451 r_mcangle_it 6.448 r_mcbond_it 5.337 r_mcbond_other 5.331 r_rigid_bond_restr 4.344 r_angle_refined_deg 1.791 r_angle_other_deg 1.486 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002 r_dihedral_angle_4_deg 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1907 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOLREP phasing XSCALE data scaling