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Crystal structure of the PDZ tandem of syntenin in complex with compound 95
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N99
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM sodium acetate
200mM ammonium acetate
20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.21 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.206 α = 90 b = 48.257 β = 120.55 c = 74.942 γ = 90
Symmetry Space Group C 1 2 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 2021-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.972423 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.469 44.01 85.72 0.05515 0.02592 0.999 17.69 5.4 9873 72.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.469 2.557 0.6629 0.3049 0.767
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 MOLECULAR REPLACEMENT THROUGHOUT 1N99 2.469 44.01 9873 498 85.8 0.2063 0.2026 0.2012 0.2792 0.2747 RANDOM 71.35
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] -0.5891 -1.0866 1.4682 -0.8791
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.3 t_omega_torsion 2.95 t_angle_deg 1.05 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.3 t_omega_torsion 2.95 t_angle_deg 1.05 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2475 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 72
Software Software Software Name Purpose SCALA data scaling BUSTER refinement PDB_EXTRACT data extraction autoPROC data reduction PHASER phasing