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SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with POB0093
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BLU 8BLU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 100 mM Morpheus amino acids, 100 mM Morpheus buffer system 1, 43% Morpheus precipitant mix 3
Crystal Properties Matthews coefficient Solvent content 2.67 53.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.342 α = 90 b = 49.174 β = 95.06 c = 116.216 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 2022-08-08 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.77 80.04 99.4 0.088 0.096 0.036 0.992 10.1 6.8 88094
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 1.77 1.8 92.8 2.72 3.019 1.279 0.336 5.4 4134
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 FOURIER SYNTHESIS THROUGHOUT 8BLU 1.77 80.04 81691 4212 96.85 0.2578 0.2556 0.2912 0.299 0.3285 RANDOM 46.11
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] 0.94 0.98 -2.14 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 18.433 r_dihedral_angle_3_deg 17.107 r_dihedral_angle_1_deg 7.9 r_angle_refined_deg 1.71 r_mcangle_it 1.632 r_angle_other_deg 1.338 r_mcbond_other 0.859 r_mcbond_it 0.855 r_chiral_restr 0.065
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.717 r_dihedral_angle_4_deg 18.433 r_dihedral_angle_3_deg 17.107 r_dihedral_angle_1_deg 7.9 r_angle_refined_deg 1.71 r_mcangle_it 1.632 r_angle_other_deg 1.338 r_mcbond_other 0.859 r_mcbond_it 0.855 r_chiral_restr 0.065 r_bond_refined_d 0.018 r_bond_other_d 0.018 r_gen_planes_refined 0.008 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5908 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing