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SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1454310449
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 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.911 α = 90 b = 49.208 β = 95.35 c = 114.396 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 2.25 113.82 99.8 0.142 0.168 0.09 0.968 10.5 3.4 42971
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 2.25 2.33 98.5 1.489 1.765 0.939 0.267 3.5 4115
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 2.25 113.82 40814 2098 99.67 0.2253 0.222 0.2461 0.2884 0.2964 RANDOM 52.958
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] 0.36 1.12 -1.32 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.292 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_3_deg 17.945 r_dihedral_angle_1_deg 8.014 r_mcangle_it 2.924 r_angle_refined_deg 1.633 r_mcbond_other 1.622 r_mcbond_it 1.596 r_angle_other_deg 1.198 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.292 r_dihedral_angle_4_deg 20.889 r_dihedral_angle_3_deg 17.945 r_dihedral_angle_1_deg 8.014 r_mcangle_it 2.924 r_angle_refined_deg 1.633 r_mcbond_other 1.622 r_mcbond_it 1.596 r_angle_other_deg 1.198 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5908 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 129
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing