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Crystal structure of the extracellular domain of neuroligin 2A from mouse
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 3.5% PEG 6000, 0.1M Bicine, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.57 65.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 214.723 α = 90 b = 92.567 β = 98.36 c = 188.408 γ = 90
Symmetry Space Group C 1 2 1
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 MAR CCD 165 mm 2007-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4C 0.9793 NSLS X4C
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 3.3 30 98.6 0.101 7.9 3.1 57279 54385
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 3.3 3.42 96.9 0.503 0.503 1.4 2.8 5279
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 3.3 20 54279 54190 2714 98.51 0.221 0.219 0.2302 0.262 0.2324 RANDOM 126.202
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] 1.45 -9.25 -2.62 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.639 r_dihedral_angle_3_deg 19.917 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_1_deg 6.05 r_angle_refined_deg 1.213 r_scangle_it 0.937 r_scbond_it 0.528 r_mcangle_it 0.51 r_nbtor_refined 0.309 r_mcbond_it 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.639 r_dihedral_angle_3_deg 19.917 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_1_deg 6.05 r_angle_refined_deg 1.213 r_scangle_it 0.937 r_scbond_it 0.528 r_mcangle_it 0.51 r_nbtor_refined 0.309 r_mcbond_it 0.278 r_symmetry_vdw_refined 0.213 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17172 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 150
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection