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The crystal structure of APRIL bound to BCMA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U5Z APRIL alone (1U5Z)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 292 well solution: 0.1M MES, 5% Peg 8000, 10% Peg 1000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.7 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.294 α = 90 b = 114.294 β = 90 c = 91.18 γ = 120
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 SBC-3 2004-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.98040 APS 19-BM
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 2.35 50 99.9 0.067 11.7 9.4 28292 28292 -3 52
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 2.35 2.43 100 0.425 3.2 7.6 2831
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 APRIL alone (1U5Z) 2.35 30 -3 28265 25409 2856 99.96 0.1815 0.18151 0.17773 0.1816 0.21313 0.2123 THIN SHELLS 29.888
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] -0.11 -0.05 -0.11 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.064 r_scangle_it 4.711 r_mcangle_it 4.084 r_scbond_it 3.077 r_mcbond_it 2.575 r_angle_refined_deg 1.22 r_angle_other_deg 0.762 r_symmetry_hbond_refined 0.232 r_nbd_other 0.229 r_symmetry_vdw_other 0.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.064 r_scangle_it 4.711 r_mcangle_it 4.084 r_scbond_it 3.077 r_mcbond_it 2.575 r_angle_refined_deg 1.22 r_angle_other_deg 0.762 r_symmetry_hbond_refined 0.232 r_nbd_other 0.229 r_symmetry_vdw_other 0.201 r_nbd_refined 0.18 r_symmetry_vdw_refined 0.142 r_xyhbond_nbd_refined 0.133 r_nbtor_other 0.083 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4082 Nucleic Acid Atoms Solvent Atoms 36 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing