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scdSav(SASK) - Engineering Single-Chain Dimeric Streptavidin as Host for Artificial Metalloenzymes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.219 α = 90 b = 57.201 β = 108.09 c = 57.201 γ = 90
Symmetry Space Group C 1 2 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 2M-F 2018-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.85 43.82 100 0.102 0.997 8 3.3 54365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 99.9 1.097 0.431 1.2 3.4
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3PK2 1.85 43.82 48458 2887 99.63 0.195 0.2043 0.231 0.1888 RANDOM 30.558
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] 2.08 0.75 -1.42 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.046 r_dihedral_angle_4_deg 20.24 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_1_deg 8.009 r_mcangle_it 4.229 r_angle_refined_deg 2.945 r_mcbond_it 2.854 r_mcbond_other 2.854 r_angle_other_deg 2.552 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.046 r_dihedral_angle_4_deg 20.24 r_dihedral_angle_3_deg 14.452 r_dihedral_angle_1_deg 8.009 r_mcangle_it 4.229 r_angle_refined_deg 2.945 r_mcbond_it 2.854 r_mcbond_other 2.854 r_angle_other_deg 2.552 r_chiral_restr 0.077 r_bond_other_d 0.038 r_gen_planes_other 0.015 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3633 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 358
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling PHASER phasing