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Crystal Structure of the alpha-Neurexin-1 ectodomain, LNS 2-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BOD PDB ENTRIES 3BOD, 2HOB, 2R16 experimental model PDB 2HOB PDB ENTRIES 3BOD, 2HOB, 2R16 experimental model PDB 2R16 PDB ENTRIES 3BOD, 2HOB, 2R16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9 287 12% PEG20000, 100 mM bicine, 1 mM EDTA, 150 mM NaCl , pH 9.0, VAPOR DIFFUSION, temperature 287K
Crystal Properties Matthews coefficient Solvent content 3.61 65.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.74 α = 90 b = 61.24 β = 121.21 c = 155.58 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 MARMOSAIC 325 mm CCD 2010-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.02 38.564 97.9 0.14 8.7 3.4 32190 31504 -3 63.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.02 3.13 99.5 0.628 2 3.4 3223
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 ENTRIES 3BOD, 2HOB, 2R16 3.02 38.56 29917 1586 98.17 0.21642 0.21356 0.2158 0.26913 0.2618 RANDOM 40.449
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] 3.09 3.05 1.24 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.038 r_dihedral_angle_3_deg 17.235 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_1_deg 7.316 r_angle_other_deg 4.284 r_angle_refined_deg 1.369 r_mcangle_it 1.235 r_mcbond_it 0.881 r_scangle_it 0.671 r_scbond_it 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.038 r_dihedral_angle_3_deg 17.235 r_dihedral_angle_4_deg 15.855 r_dihedral_angle_1_deg 7.316 r_angle_other_deg 4.284 r_angle_refined_deg 1.369 r_mcangle_it 1.235 r_mcbond_it 0.881 r_scangle_it 0.671 r_scbond_it 0.46 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7791 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 50
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling