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SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z56772132
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 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.04 α = 90 b = 49.508 β = 94.74 c = 115.578 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 2022-04-14 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9179 Diamond I04-1
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 2.02 115.22 99.9 0.119 0.142 0.075 0.97 11.4 3.5 60354
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 2.02 2.08 98.4 1.249 1.473 0.775 0.332 3.6 4571
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 8BLU 2.02 115.18 57348 2936 99.73 0.203 0.2005 0.2523 0.2292 RANDOM 42.955
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] -0.7 0.63 -0.97 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.801 r_dihedral_angle_4_deg 20.263 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_1_deg 7.622 r_mcangle_it 3.117 r_mcbond_other 1.88 r_mcbond_it 1.879 r_angle_refined_deg 1.778 r_angle_other_deg 1.296 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.801 r_dihedral_angle_4_deg 20.263 r_dihedral_angle_3_deg 17.12 r_dihedral_angle_1_deg 7.622 r_mcangle_it 3.117 r_mcbond_other 1.88 r_mcbond_it 1.879 r_angle_refined_deg 1.778 r_angle_other_deg 1.296 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5908 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing