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Crystal Structure of bovine neurexin 1 alpha LNS/LG domain 4 (with no splice insert)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C4R PDB entry 1C4R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 293 12.5% isopropanol, 0.1 M CHES pH 9.0, 5 mM CaCl2, , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.322 α = 90 b = 90.322 β = 90 c = 39.624 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD MARMOSAIC 300 mm CCD 2006-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96112 APS 23-ID-B
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 1.04 23.7 92.9 0.07 37.9 12.6 82197 82197 7.5
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) 1.04 1.08 60.5 0.296 0.296 6.2 7.6 5319
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1C4R 1.04 23.7 80871 72763 8108 100 0.14839 0.14839 0.1465 0.2346 0.16518 0.2441 RANDOM 11.292
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] -0.08 -0.04 -0.08 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.14 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_4_deg 10.121 r_sphericity_free 8.859 r_dihedral_angle_1_deg 7.896 r_scangle_it 3.966 r_sphericity_bonded 3.947 r_scbond_it 2.964 r_mcangle_it 2.35 r_angle_other_deg 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.14 r_dihedral_angle_3_deg 12.328 r_dihedral_angle_4_deg 10.121 r_sphericity_free 8.859 r_dihedral_angle_1_deg 7.896 r_scangle_it 3.966 r_sphericity_bonded 3.947 r_scbond_it 2.964 r_mcangle_it 2.35 r_angle_other_deg 1.93 r_angle_refined_deg 1.906 r_mcbond_it 1.659 r_rigid_bond_restr 1.389 r_mcbond_other 0.68 r_symmetry_hbond_refined 0.425 r_symmetry_vdw_other 0.332 r_nbd_refined 0.226 r_nbd_other 0.217 r_symmetry_vdw_refined 0.215 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.115 r_nbtor_other 0.094 r_metal_ion_refined 0.06 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1476 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing