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Crystal Structure of the second LNS/LG domain from Neurexin 1 alpha
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 294 10% P8000, 0.1M Tris, 5mM CaCl2, 1% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.032 α = 78.47 b = 61.586 β = 78.74 c = 66.64 γ = 84.68
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 ADSC QUANTUM 210 2005-05-01 M MAD 2 1 3 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F2 0.978952, 0.979338, 0.980111 CHESS F2
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 2.1 40 96.6 0.072 11.3 3.6 51547
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 2.1 2.18 85.9 0.265 2.7 4563
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.1 20 51492 2577 100 0.186 0.18607 0.184 0.233 0.2491 RANDOM 36.373
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] 1.21 3.82 -0.68 0.15 -0.71 -1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.836 r_dihedral_angle_4_deg 20.045 r_dihedral_angle_3_deg 13.908 r_dihedral_angle_1_deg 7.085 r_scangle_it 3.005 r_scbond_it 2.014 r_angle_refined_deg 1.391 r_mcangle_it 1.042 r_mcbond_it 0.741 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.836 r_dihedral_angle_4_deg 20.045 r_dihedral_angle_3_deg 13.908 r_dihedral_angle_1_deg 7.085 r_scangle_it 3.005 r_scbond_it 2.014 r_angle_refined_deg 1.391 r_mcangle_it 1.042 r_mcbond_it 0.741 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.253 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.217 r_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.133 r_chiral_restr 0.086 r_symmetry_metal_ion_refined 0.068 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5553 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction