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SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z27782662
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 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.12 α = 90 b = 49.37 β = 94.61 c = 115.54 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 1.8 57.58 100 0.061 0.066 0.025 0.999 11.7 6.9 84032
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 1.8 1.85 99.9 2.922 3.205 1.291 0.348 6 6203
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 1.8 57.58 79807 4112 99.78 0.2922 0.2887 0.2944 0.3589 0.3618 RANDOM 53.156
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] -2.22 0.83 -1.24 3.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.512 r_dihedral_angle_2_deg 8.094 r_dihedral_angle_1_deg 7.816 r_mcangle_it 7.381 r_mcbond_it 5.514 r_mcbond_other 5.513 r_angle_refined_deg 1.454 r_angle_other_deg 0.475 r_chiral_restr 0.065 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.512 r_dihedral_angle_2_deg 8.094 r_dihedral_angle_1_deg 7.816 r_mcangle_it 7.381 r_mcbond_it 5.514 r_mcbond_other 5.513 r_angle_refined_deg 1.454 r_angle_other_deg 0.475 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5908 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing