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Structure of neurexin 1 alpha (domains LNS1-LNS6), with splice insert SS3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QCW PDB ENTRY 3QCW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 4.04 69.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.03 α = 89.6 b = 114.574 β = 89.98 c = 160.129 γ = 87.96
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD 2010-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1272 APS 21-ID-D
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 2.95 50 98.4 0.09 10 3.4 89668
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 2.95 3 95.6 0.532 3.1 4356
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 PDB ENTRY 3QCW 2.95 44.29 89495 4654 98.15 0.2097 0.2083 0.2025 0.2353 0.2312 RANDOM 92.1204
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] -7.06 0.84 -1.09 -2.87 -0.42 9.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.83 r_dihedral_angle_3_deg 20.69 r_dihedral_angle_4_deg 20.317 r_dihedral_angle_1_deg 9.096 r_scangle_it 2.787 r_angle_refined_deg 2.335 r_scbond_it 1.902 r_mcangle_it 1.187 r_mcbond_it 0.717 r_nbtor_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.83 r_dihedral_angle_3_deg 20.69 r_dihedral_angle_4_deg 20.317 r_dihedral_angle_1_deg 9.096 r_scangle_it 2.787 r_angle_refined_deg 2.335 r_scbond_it 1.902 r_mcangle_it 1.187 r_mcbond_it 0.717 r_nbtor_refined 0.336 r_symmetry_vdw_refined 0.288 r_symmetry_hbond_refined 0.279 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.139 r_bond_refined_d 0.026 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15466 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction