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Hoefavidin P61C mutant generates a stabilized octamer
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 1.5-1.8 M LI2SO4 AND 0.1 M HEPES (PH 7.5-7.7)
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.885 α = 90 b = 81.885 β = 90 c = 130.429 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 PILATUS3 S 6M optical hutch 2017-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.978 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 2 43.48 99.7 0.04 17.8 6.1 18089
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 2.05 99.1 0.784
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 2 40.98 17153 891 99.5 0.23 0.227 0.2386 0.283 0.2943 RANDOM 56.13
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] -1.16 -0.58 -1.16 3.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.377 r_dihedral_angle_3_deg 17.028 r_long_range_B_other 12.627 r_long_range_B_refined 12.624 r_scangle_other 10.51 r_dihedral_angle_1_deg 9.395 r_mcangle_it 9.395 r_mcangle_other 9.393 r_scbond_it 7.936 r_scbond_other 7.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.377 r_dihedral_angle_3_deg 17.028 r_long_range_B_other 12.627 r_long_range_B_refined 12.624 r_scangle_other 10.51 r_dihedral_angle_1_deg 9.395 r_mcangle_it 9.395 r_mcangle_other 9.393 r_scbond_it 7.936 r_scbond_other 7.935 r_mcbond_it 7.669 r_mcbond_other 7.667 r_angle_refined_deg 2.08 r_angle_other_deg 1.463 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1996 Nucleic Acid Atoms Solvent Atoms 77 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing