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The Crystal structure of murine APRIL, pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OSG truncated model of BAFF (pdb entry 1OSG)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 0.1 M Tris, pH 8.5, 0.5 M KSCN, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.1 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.166 α = 90 b = 92.166 β = 90 c = 92.166 γ = 90
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 4 2003-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.4 50 99 0.043 15.4 6.7 5238 5238 -3 60
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 2.4 2.49 100 0.461 3.2 6.7 510
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 truncated model of BAFF (pdb entry 1OSG) 2.4 29.11 -3 5231 5231 506 99.94 0.2232 0.2232 0.21866 0.2217 0.26452 0.2725 Random 32.341
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.824 r_dihedral_angle_3_deg 17.162 r_dihedral_angle_4_deg 14.361 r_dihedral_angle_1_deg 6.629 r_scangle_it 3.746 r_mcangle_it 2.76 r_scbond_it 2.418 r_mcbond_it 1.801 r_angle_refined_deg 1.157 r_angle_other_deg 0.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.824 r_dihedral_angle_3_deg 17.162 r_dihedral_angle_4_deg 14.361 r_dihedral_angle_1_deg 6.629 r_scangle_it 3.746 r_mcangle_it 2.76 r_scbond_it 2.418 r_mcbond_it 1.801 r_angle_refined_deg 1.157 r_angle_other_deg 0.706 r_symmetry_vdw_refined 0.296 r_xyhbond_nbd_refined 0.288 r_symmetry_vdw_other 0.243 r_nbd_other 0.234 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.118 r_nbtor_other 0.082 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 988 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing