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Crystal structure of a Tip20p-Dsl1p fusion protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ETU PDB entry 3ETU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 298 5:5:1 ratio of protein, well buffer (0.1 M sodium acetate, pH 5.0, 0.2 M ammonium acetate, 20% (w/v) PEG 4000), and additive (1.0 M lithium chloride) , VAPOR DIFFUSION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.43 α = 90 b = 61.358 β = 91.96 c = 37.277 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 315 2008-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0400 NSLS X25
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 1.94 100 90.7 0.057 18 3.1 25475
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) 1.94 2.02 97 0.467 2 2.9 2691
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 3ETU 1.94 40 24166 1281 90.35 0.22737 0.22453 0.2237 0.27722 0.2737 RANDOM 28.559
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] 0.73 0.11 -1.35 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.886 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_1_deg 5.44 r_scangle_it 3.516 r_mcangle_it 3.328 r_scbond_it 2.63 r_mcbond_it 2.417 r_angle_refined_deg 1.091 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.886 r_dihedral_angle_4_deg 20.888 r_dihedral_angle_3_deg 13.308 r_dihedral_angle_1_deg 5.44 r_scangle_it 3.516 r_mcangle_it 3.328 r_scbond_it 2.63 r_mcbond_it 2.417 r_angle_refined_deg 1.091 r_nbtor_refined 0.295 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.175 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.131 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2566 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling