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Crystal structure of PSD-95 PDZ3 fused with ADAM22 C-terminal peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2 M choline chloride, 0.1 M Tris-HCl (pH 7.5), 14 % (w/v) PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.75 29.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.961 α = 90 b = 63.961 β = 90 c = 48.795 γ = 120
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 EIGER X 16M 2019-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 100 0.13 0.134 0.031 0.999 26.2 16.1 10624
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 0.745 0.791 0.262 0.944
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TP3 1.8 36.64 10052 548 99.99 0.16893 0.16684 0.20513 0.2033 RANDOM 31.53
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] 0.54 0.27 0.54 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.697 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 15.046 r_long_range_B_refined 8.071 r_long_range_B_other 8.071 r_dihedral_angle_1_deg 7.08 r_scangle_other 6.361 r_scbond_it 4.08 r_scbond_other 4.076 r_mcangle_other 3.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.697 r_dihedral_angle_4_deg 17.496 r_dihedral_angle_3_deg 15.046 r_long_range_B_refined 8.071 r_long_range_B_other 8.071 r_dihedral_angle_1_deg 7.08 r_scangle_other 6.361 r_scbond_it 4.08 r_scbond_other 4.076 r_mcangle_other 3.549 r_mcangle_it 3.548 r_mcbond_it 2.521 r_mcbond_other 2.511 r_angle_refined_deg 1.66 r_angle_other_deg 1.413 r_chiral_restr 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 877 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing