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Crystal structure of the chicken MDGA1 ectodomain in complex with the human neuroligin 1 (NL1(-A-B)) cholinesterase domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Na.HEPES pH 7.0, 7.5% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.92 57.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.42 α = 90 b = 184.14 β = 90 c = 96.47 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 6M 2014-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.3 92.07 98.7 0.999 15.6 4.5 29576
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.39 95.4 1.063 0.638 1.6 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5OJ2 3.3 72.362 1.34 29572 1474 98.41 0.2294 0.2269 0.2336 0.2771 0.2779
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.487 f_angle_d 0.939 f_chiral_restr 0.041 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9659 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 151
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing