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Apo structure of BIR2 Domain of BIRC2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q13490-F1 AF-Q13490-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 8 mg/mL protein
23% PEG Smear broad, 0.1 Na/K tartrate, 12 % Ethylenglycol, cacodylate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.241 α = 90 b = 87.241 β = 90 c = 59.625 γ = 120
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 EIGER X 16M 2021-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.999998 SLS X06SA
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 1.3 46.81 99 0.07 0.08 0.038 0.989 13.1 5 41245
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 1.3 1.32 98 0.849 0.973 0.464 0.823 4.2
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 AF-Q13490-F1 1.3 46.81 39167 2076 99.03 0.1431 0.1424 0.1498 0.1552 0.17 RANDOM 23.141
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] -0.23 -0.12 -0.23 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.524 r_dihedral_angle_4_deg 16.011 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.038 r_angle_refined_deg 1.427 r_angle_other_deg 1.349 r_rigid_bond_restr 0.907 r_chiral_restr 0.071 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.524 r_dihedral_angle_4_deg 16.011 r_dihedral_angle_3_deg 12.575 r_dihedral_angle_1_deg 6.038 r_angle_refined_deg 1.427 r_angle_other_deg 1.349 r_rigid_bond_restr 0.907 r_chiral_restr 0.071 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1262 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 42
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction