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Crystal structure of apo intact hoefavidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.5-1.8 M Li2SO4 and 0.1 M HEPES (pH 7.5-7.7)
Crystal Properties Matthews coefficient Solvent content 2.05 40.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.01 α = 90 b = 82.01 β = 90 c = 130.1 γ = 120
Symmetry Space Group P 62 2 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 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 2.4 50 99.6 0.041 38 11.1 10687
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 2.4 2.49 0.227
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 3ew1 2.4 47.97 10131 520 99.62 0.23515 0.23249 0.2387 0.28945 0.2894 RANDOM 48.032
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] -0.71 -0.35 -0.71 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.596 r_dihedral_angle_3_deg 18.219 r_dihedral_angle_1_deg 8.322 r_long_range_B_refined 6.973 r_long_range_B_other 6.832 r_angle_refined_deg 1.657 r_mcangle_it 1.647 r_mcangle_other 1.646 r_scangle_other 1.345 r_angle_other_deg 1.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.596 r_dihedral_angle_3_deg 18.219 r_dihedral_angle_1_deg 8.322 r_long_range_B_refined 6.973 r_long_range_B_other 6.832 r_angle_refined_deg 1.657 r_mcangle_it 1.647 r_mcangle_other 1.646 r_scangle_other 1.345 r_angle_other_deg 1.326 r_mcbond_other 0.967 r_mcbond_it 0.966 r_scbond_it 0.782 r_scbond_other 0.779 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1980 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOLREP phasing XSCALE data scaling