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Streptavidin Iron-Porphyrin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RY2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M MIB 7 pH (Buffer)
22.5 %v/v PEG 1500 (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.251 α = 90 b = 89.439 β = 97.54 c = 57.167 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 2021-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00003 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.74 46.01 100 0.05 0.059 0.031 1 20.1 6.9 58882
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 1.4 1.648 0.862 0.521 7.1
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 3ry2 1.74 44.76 55945 2936 99.98 0.1714 0.1697 0.1794 0.2035 0.2101 RANDOM 33.568
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] 0.21 0.56 0.4 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 13.885 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 7.863 r_angle_refined_deg 1.564 r_angle_other_deg 0.615 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3646 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing