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Crystal structure of 14-3-3 in complex with PyrinpS242 and a protein/peptide interface fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 0.19 M CaCl 2 ,
5% glycerol, 26% PEG 400, 0.095 M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.142 α = 90 b = 111.969 β = 90 c = 62.477 γ = 90
Symmetry Space Group C 2 2 21
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 2020-06-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033215 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.4 62.48 98.1 0.998 20.5 6.4 55917
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 0.948
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE in house 1.4 45.488 55891 2813 98.127 0.181 0.1793 0.1878 0.2039 0.2087 16.007
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] 0.817 -0.363 -0.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_3_deg 11.66 r_lrange_it 5.409 r_dihedral_angle_1_deg 5.37 r_lrange_other 5.288 r_scangle_it 3.672 r_scangle_other 3.672 r_mcangle_it 2.627 r_mcangle_other 2.626
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_3_deg 11.66 r_lrange_it 5.409 r_dihedral_angle_1_deg 5.37 r_lrange_other 5.288 r_scangle_it 3.672 r_scangle_other 3.672 r_mcangle_it 2.627 r_mcangle_other 2.626 r_scbond_it 2.512 r_scbond_other 2.512 r_angle_refined_deg 2.004 r_mcbond_it 1.675 r_mcbond_other 1.675 r_angle_other_deg 1.662 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.249 r_nbtor_refined 0.185 r_symmetry_nbd_other 0.182 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.13 r_symmetry_xyhbond_nbd_refined 0.126 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.038 r_symmetry_metal_ion_refined 0.038 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1860 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing