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SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with POB0008
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 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.693 α = 90 b = 49.422 β = 95.15 c = 114.672 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 1.85 80.32 99.7 0.125 0.135 0.051 0.997 6.6 6.8 77319
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 1.85 1.89 95.7 2.987 3.236 1.232 0.65 6.8 4365
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 1.85 80.32 69044 3544 93.89 0.2173 0.215 0.2249 0.2621 0.2624 RANDOM 45.556
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] -0.6 0.21 0.62 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 20.871 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_1_deg 7.994 r_mcangle_it 3.039 r_mcbond_other 1.782 r_mcbond_it 1.765 r_angle_refined_deg 1.742 r_angle_other_deg 1.277 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.111 r_dihedral_angle_4_deg 20.871 r_dihedral_angle_3_deg 16.878 r_dihedral_angle_1_deg 7.994 r_mcangle_it 3.039 r_mcbond_other 1.782 r_mcbond_it 1.765 r_angle_refined_deg 1.742 r_angle_other_deg 1.277 r_chiral_restr 0.077 r_bond_refined_d 0.01 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 343 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing