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Crystal structure of beta-neurexin 2 with the splice insert 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BOP PDB ID 3BOP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 22% PEG3350, 0.35M calcium chloride, 1mM GSH/GSSG, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.657 α = 90 b = 102.087 β = 90 c = 78.512 γ = 90
Symmetry Space Group C 2 2 21
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 MAR CCD 165 mm Si (111) crystal monochromator with vertical focusing mirror 2009-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9795 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.35 50 96.7 0.088 0.088 28.8 5.8 9191 8885 1 1
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 (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 ID 3BOP 2.33 19.25 8553 433 98.28 0.194 0.19395 0.19083 0.189 0.25248 0.2432 RANDOM 34.77
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] -0.15 -0.39 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.065 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 16.047 r_dihedral_angle_1_deg 7.364 r_scangle_it 3.081 r_scbond_it 1.949 r_angle_refined_deg 1.555 r_mcangle_it 1.327 r_mcbond_it 0.737 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.065 r_dihedral_angle_4_deg 19.017 r_dihedral_angle_3_deg 16.047 r_dihedral_angle_1_deg 7.364 r_scangle_it 3.081 r_scbond_it 1.949 r_angle_refined_deg 1.555 r_mcangle_it 1.327 r_mcbond_it 0.737 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.296 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.22 r_xyhbond_nbd_refined 0.191 r_chiral_restr 0.101 r_metal_ion_refined 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1474 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 41
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling