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SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1650168321
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 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.444 α = 90 b = 49.502 β = 95.4 c = 114.424 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 1.86 80.09 99.9 0.106 0.125 0.066 0.982 13.4 3.5 75903
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 1.86 1.9 99.5 1.651 1.985 1.092 0.316 3.2 4455
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 1.86 80.09 72084 3707 99.75 0.1985 0.1964 0.2109 0.2393 0.2498 RANDOM 42.513
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] -0.58 1.72 -1.01 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.806 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 16.203 r_dihedral_angle_1_deg 7.877 r_mcangle_it 3.465 r_mcbond_it 2.118 r_mcbond_other 2.117 r_angle_refined_deg 1.798 r_angle_other_deg 1.316 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.806 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 16.203 r_dihedral_angle_1_deg 7.877 r_mcangle_it 3.465 r_mcbond_it 2.118 r_mcbond_other 2.117 r_angle_refined_deg 1.798 r_angle_other_deg 1.316 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 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 372 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing