☰ Navigation Tabs
Crystal structure of APRIL bound to a peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XU1 Chain A from pdb 1xu1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 2ul drops of protein (5 mg/mg. at pH 9.7) was added to 2 uL of 4M formate. Crystals formed immediately, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.2 44.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.811 α = 90 b = 84.771 β = 99.45 c = 55.562 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 CCD ADSC QUANTUM 210 2005-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1
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 2.8 50 99.6 0.108 12.4 3.7 11453 11453 -3 50
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 2.8 2.9 98.4 0.506 2.5 3.6 1126
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 (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 Chain A from pdb 1xu1 2.8 30 10257 1143 99.59 0.21169 0.20548 0.209 0.2669 0.2701 thin shells 16.768
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] -0.37 -1.52 -2.51 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.822 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_3_deg 15.047 r_dihedral_angle_1_deg 6.842 r_mcangle_it 2.929 r_scangle_it 2.872 r_mcbond_it 2.345 r_scbond_it 1.788 r_angle_refined_deg 1.252 r_angle_other_deg 0.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.822 r_dihedral_angle_4_deg 17.592 r_dihedral_angle_3_deg 15.047 r_dihedral_angle_1_deg 6.842 r_mcangle_it 2.929 r_scangle_it 2.872 r_mcbond_it 2.345 r_scbond_it 1.788 r_angle_refined_deg 1.252 r_angle_other_deg 0.953 r_mcbond_other 0.494 r_symmetry_vdw_other 0.294 r_symmetry_vdw_refined 0.237 r_nbd_other 0.198 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.181 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.079 r_nbtor_other 0.079 r_bond_refined_d 0.01 r_bond_other_d 0.004 r_gen_planes_refined 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3613 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling