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Crystal structure of FASL and DcR3 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J6G PDB ENTRY 4J6G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 0.09M Malonic Acid, 0.013M Ammonium Citr Tribasic, 0.006M Succinic Acid, 0.015M DL-Malic Acid, 0.02M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, Final pH 7.0; 0.1M HEPES:NaOH pH 7.0, 10% (w/v) PEG MME 5000, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 1.46 15.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.909 α = 90 b = 126.909 β = 90 c = 205.729 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 ADSC QUANTUM 315 2013-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.5 50 100 0.116 0.092 14.9 7.3 22326
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 99.8 0.826 0.773 2 7
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 PDB ENTRY 4J6G 2.5 48.52 21164 1144 99.38 0.18914 0.18744 0.192 0.22075 0.2233 RANDOM 45.065
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] -0.34 -0.34 -0.34 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.489 r_dihedral_angle_3_deg 18.565 r_dihedral_angle_4_deg 17.612 r_dihedral_angle_1_deg 7.468 r_angle_refined_deg 2.036 r_angle_other_deg 0.969 r_chiral_restr 0.13 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.489 r_dihedral_angle_3_deg 18.565 r_dihedral_angle_4_deg 17.612 r_dihedral_angle_1_deg 7.468 r_angle_refined_deg 2.036 r_angle_other_deg 0.969 r_chiral_restr 0.13 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2332 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms 7
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling