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Crystal structure of MAGI2 PDZ0-GK domain in complex with phospho-SAPAP1 GBR3 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EEH 2EEH,5YPO experimental model PDB 5YPO 2EEH,5YPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 2.1 M ammonium phosphate dibasic, 0.2 M ammonium sulfate, 0.1M Tris (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.19 43.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.975 α = 90 b = 78.909 β = 90 c = 92.997 γ = 90
Symmetry Space Group P 21 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97930 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 50 97.3 0.091 12.9 4.3 32529
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 98.9 0.506 4.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2EEH,5YPO 2 44.496 32474 1601 96.94 0.209 0.2074 0.216 0.2486 0.2503 28.078
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] 4.342 -2.295 -2.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.143 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_2_deg 12.674 r_lrange_it 8.682 r_lrange_other 8.578 r_dihedral_angle_1_deg 6.835 r_scangle_it 6.097 r_scangle_other 6.096 r_mcangle_it 4.329 r_mcangle_other 4.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.143 r_dihedral_angle_3_deg 14.466 r_dihedral_angle_2_deg 12.674 r_lrange_it 8.682 r_lrange_other 8.578 r_dihedral_angle_1_deg 6.835 r_scangle_it 6.097 r_scangle_other 6.096 r_mcangle_it 4.329 r_mcangle_other 4.329 r_scbond_it 3.928 r_scbond_other 3.927 r_mcbond_it 2.887 r_mcbond_other 2.883 r_angle_refined_deg 1.489 r_angle_other_deg 0.496 r_xyhbond_nbd_refined 0.248 r_nbd_refined 0.217 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.178 r_nbd_other 0.178 r_symmetry_xyhbond_nbd_other 0.152 r_ncsr_local_group_2 0.147 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_nbd_refined 0.131 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.067 r_ncsr_local_group_1 0.059 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3006 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction DENZO data reduction PHASER phasing