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Crystal structure of apo short hoefavidin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z6J
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 54.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.17 α = 90 b = 61.17 β = 90 c = 166.62 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 2013-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.98 ESRF ID23-1
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 1.34 57.4 95.6 0.047 27.1 13.8 72099
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 1.34 1.39 0.564
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 4Z6J 1.34 57.42 65432 3408 95.59 0.16634 0.1652 0.1751 0.18904 0.198 RANDOM 22.422
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] 0.42 0.42 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.633 r_sphericity_free 23.745 r_dihedral_angle_3_deg 12.484 r_sphericity_bonded 12.351 r_dihedral_angle_1_deg 6.706 r_long_range_B_refined 4.67 r_long_range_B_other 4.65 r_mcangle_it 4.311 r_mcangle_other 4.31 r_rigid_bond_restr 4.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.633 r_sphericity_free 23.745 r_dihedral_angle_3_deg 12.484 r_sphericity_bonded 12.351 r_dihedral_angle_1_deg 6.706 r_long_range_B_refined 4.67 r_long_range_B_other 4.65 r_mcangle_it 4.311 r_mcangle_other 4.31 r_rigid_bond_restr 4.072 r_scangle_other 3.947 r_mcbond_it 3.428 r_mcbond_other 3.419 r_scbond_it 3.396 r_scbond_other 3.395 r_angle_refined_deg 1.457 r_angle_other_deg 0.947 r_chiral_restr 0.096 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 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 1892 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOLREP phasing XSCALE data scaling