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Crystal Structure of the 3rd PDZ domain of the human Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 3 (MAGI3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BPU Ensemble of 3BPU, 2R4H, 2Q9V experimental model PDB 2R4H Ensemble of 3BPU, 2R4H, 2Q9V experimental model PDB 2Q9V Ensemble of 3BPU, 2R4H, 2Q9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1M Bis-tris pH 6.0
0.25M Li2SO4
35% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.79 55.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.63 α = 90 b = 59.28 β = 90 c = 65.35 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV 2011-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.52
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 22.52 97.9 0.046 0.046 17.1 4.7 18521 18132 23.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.68 95 0.515 0.515 1.5 3.8 2491
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Ensemble of 3BPU, 2R4H, 2Q9V 1.6 22.52 18532 18095 924 97.64 0.1894 0.1894 0.188 0.2164 0.2171 RANDOM 23.4798
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] 1.14 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_4_deg 20.595 r_dihedral_angle_3_deg 12.033 r_scangle_it 6.467 r_dihedral_angle_1_deg 5.469 r_scbond_it 4.211 r_mcangle_it 2.74 r_mcbond_it 1.576 r_angle_refined_deg 1.403 r_angle_other_deg 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.489 r_dihedral_angle_4_deg 20.595 r_dihedral_angle_3_deg 12.033 r_scangle_it 6.467 r_dihedral_angle_1_deg 5.469 r_scbond_it 4.211 r_mcangle_it 2.74 r_mcbond_it 1.576 r_angle_refined_deg 1.403 r_angle_other_deg 0.887 r_mcbond_other 0.449 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 765 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 4
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection MOSFLM data reduction