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X-ray crystal structure of allo-Thr31-ShK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.2 M Ammonium sulfate,
0.1 M BIS-TRIS
25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.743 α = 90 b = 46.229 β = 108.02 c = 40.064 γ = 90
Symmetry Space Group P 1 21 1
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-F 2015-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.7749 APS 24-ID-C
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 1.3 38.1 97.8 0.061 9.5 3.4 31126
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 1.3 1.32 99.6 0.65 1.7 3.5
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 4LFQ 1.3 38.1 24495 1312 97.89 0.12951 0.12738 0.1691 0.1647 RANDOM 17.512
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] -1.03 -1.24 1.51 0.28
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 56.14 r_dihedral_angle_2_deg 29.605 r_sphericity_bonded 21.315 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_3_deg 10.788 r_rigid_bond_restr 7.536 r_dihedral_angle_1_deg 6.161 r_long_range_B_refined 5.742 r_scbond_it 4.506 r_angle_refined_deg 2.905
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 56.14 r_dihedral_angle_2_deg 29.605 r_sphericity_bonded 21.315 r_dihedral_angle_4_deg 13.638 r_dihedral_angle_3_deg 10.788 r_rigid_bond_restr 7.536 r_dihedral_angle_1_deg 6.161 r_long_range_B_refined 5.742 r_scbond_it 4.506 r_angle_refined_deg 2.905 r_mcangle_it 2.082 r_mcbond_it 1.867 r_chiral_restr 0.717 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 834 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing