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Crystal structure of short hoefavidin-hoef-peptide 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 0.1 M NaCl, 0.1 M Bis-Tris pH 6.2-7.0 and 1.1-1.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.47 50.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.74 α = 90 b = 60.74 β = 90 c = 166.8 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 2013-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.39 57.07 95 0.032 19.4 5.2 61114
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.39 1.43
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 1.39 57.07 57864 3089 95.48 0.16161 0.16024 0.18659 0.196 RANDOM 21.808
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] 0.27 0.27 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.396 r_sphericity_free 23.994 r_dihedral_angle_3_deg 13.025 r_sphericity_bonded 11.809 r_dihedral_angle_1_deg 6.837 r_rigid_bond_restr 6.394 r_long_range_B_refined 5.311 r_long_range_B_other 5.302 r_scangle_other 5.001 r_mcangle_it 4.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.396 r_sphericity_free 23.994 r_dihedral_angle_3_deg 13.025 r_sphericity_bonded 11.809 r_dihedral_angle_1_deg 6.837 r_rigid_bond_restr 6.394 r_long_range_B_refined 5.311 r_long_range_B_other 5.302 r_scangle_other 5.001 r_mcangle_it 4.572 r_mcangle_other 4.571 r_scbond_it 4.2 r_scbond_other 4.164 r_mcbond_other 3.839 r_mcbond_it 3.838 r_angle_refined_deg 1.51 r_angle_other_deg 0.832 r_chiral_restr 0.101 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2056 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOLREP phasing XDS data reduction XSCALE data scaling