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Crystal Structure of rat neurexin 1beta with a splice insert at SS#4
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 8.5 277 17% Peg 8000, 0.1 M Tris pH 8.5, 0.2 M MgCl2, 5 mM CaCl2, 0.5% beta-octyl-glucoside, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.122 α = 90 b = 39.26 β = 115.47 c = 85.41 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2005-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 32-ID 1.000 APS 32-ID
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 1.72 19.9 92.1 0.054 25.9 8.2 49680 49680 22.5
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 1.72 1.76 73.1 0.355 0.355 3.1 3.5 2877
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 1.72 19.9 49679 45909 3770 100 0.19956 0.19956 0.19745 0.2021 0.22474 0.2274 RANDOM 26.719
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] -1.48 -0.91 -0.17 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.397 r_dihedral_angle_4_deg 21.441 r_dihedral_angle_3_deg 14.345 r_dihedral_angle_1_deg 6.26 r_scangle_it 4.158 r_scbond_it 2.76 r_mcangle_it 1.725 r_angle_refined_deg 1.708 r_mcbond_it 1.24 r_symmetry_hbond_refined 0.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.397 r_dihedral_angle_4_deg 21.441 r_dihedral_angle_3_deg 14.345 r_dihedral_angle_1_deg 6.26 r_scangle_it 4.158 r_scbond_it 2.76 r_mcangle_it 1.725 r_angle_refined_deg 1.708 r_mcbond_it 1.24 r_symmetry_hbond_refined 0.443 r_nbtor_refined 0.295 r_symmetry_vdw_refined 0.253 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.157 r_metal_ion_refined 0.055 r_bond_refined_d 0.023 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2980 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement CNS refinement MAR345 data collection MOSFLM data reduction SCALA data scaling CNS phasing