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Crystal structure of murine APRIL at pH 5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U5Z APRIL at pH 8.5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 292 0.1 M Citric Acid, 1.0 M LiCL, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.1 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.779 α = 90 b = 90.779 β = 90 c = 90.779 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 IMAGE PLATE MARRESEARCH osmic mirrors 2004-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 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 1.8 30 100 0.042 30.8 8.5 11701 11701 -3 30
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 1.8 1.86 100 0.442 5 5.5 1162
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 APRIL at pH 8.5 1.8 30 11701 11697 1136 99.97 0.2179 0.21799 0.21375 0.2053 0.2563 0.2484 RANDOM 19.636
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 27.584 r_dihedral_angle_4_deg 24.941 r_dihedral_angle_3_deg 15.216 r_dihedral_angle_1_deg 6.739 r_scangle_it 5.559 r_scbond_it 3.852 r_mcangle_it 3.604 r_mcbond_it 2.57 r_angle_refined_deg 1.511 r_angle_other_deg 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.584 r_dihedral_angle_4_deg 24.941 r_dihedral_angle_3_deg 15.216 r_dihedral_angle_1_deg 6.739 r_scangle_it 5.559 r_scbond_it 3.852 r_mcangle_it 3.604 r_mcbond_it 2.57 r_angle_refined_deg 1.511 r_angle_other_deg 0.828 r_symmetry_vdw_other 0.302 r_nbd_other 0.257 r_symmetry_vdw_refined 0.231 r_symmetry_hbond_refined 0.211 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.091 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 994 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing