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Complex of NLGN2 with MDGA1 Ig1-Ig2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.05 M HEPES pH 7.5, 0.05 M MOPS pH 7.5, 12 % (v/v) ethylene glycol, 9 % (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.44 64.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.118 α = 95.52 b = 97.182 β = 80.97 c = 190.51 γ = 88.71
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 225 mm CCD 2016-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 4.11 49.77 94.4 0.064 18.8 3.8 53553
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 4.11 4.18 76.1 0.586 3.5
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 3BL8 4.11 49.77 43940 2200 81.29 0.29032 0.28887 0.2874 0.31861 0.3136 RANDOM 112.283
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] -1.26 0.59 0.79 15.66 -6.26 -11.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.257 r_dihedral_angle_3_deg 20.174 r_dihedral_angle_4_deg 17.476 r_dihedral_angle_1_deg 9.001 r_angle_refined_deg 1.55 r_angle_other_deg 1.115 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.257 r_dihedral_angle_3_deg 20.174 r_dihedral_angle_4_deg 17.476 r_dihedral_angle_1_deg 9.001 r_angle_refined_deg 1.55 r_angle_other_deg 1.115 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.003 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33540 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing