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Crystal structure of murine APRIL, pH 8.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OSG I23 structure of APRIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 292 0.1 M Tris pH 8.0, 1M LiCl, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.6 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.344 α = 90 b = 81.166 β = 111.79 c = 53.585 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 IMAGE PLATE MARRESEARCH osmic mirrors 2004-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.3 50 94.5 0.06 14.7 3.8 23803 23803 -3 37
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 2.3 2.38 93 0.275 4.3 3.8 2034
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 I23 structure of APRIL 2.3 30 20737 20737 2210 94.69 0.208 0.20802 0.20075 0.207 0.26805 0.268 Thin Shells 14.653
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] 2.34 0.92 -2.02 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.786 r_scangle_it 4.613 r_mcangle_it 4.062 r_scbond_it 3.068 r_mcbond_it 2.664 r_angle_refined_deg 1.358 r_angle_other_deg 0.781 r_symmetry_vdw_other 0.249 r_nbd_other 0.238 r_nbd_refined 0.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.786 r_scangle_it 4.613 r_mcangle_it 4.062 r_scbond_it 3.068 r_mcbond_it 2.664 r_angle_refined_deg 1.358 r_angle_other_deg 0.781 r_symmetry_vdw_other 0.249 r_nbd_other 0.238 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.167 r_symmetry_vdw_refined 0.15 r_symmetry_hbond_refined 0.134 r_nbtor_other 0.085 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3139 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing