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Crystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317 Fused to MBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PEB PDB Code:1PEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 5 298 Crystals were grown at 25C by using microbatch under oil by mixing protein with crystallization buffer containing 100 mM sodium acetate (pH 5.0), 200 mM
NaCl, 20% PEG 6000. Micro batch under oil, pH 5.0, EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.46 49.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.502 α = 90 b = 202.443 β = 90.41 c = 107.277 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315r 2010-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0091 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 2.8 42.47 96 0.116 0.116 11.6 3.5 94908 -3 27
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) 2.8 2.9 90.4 1 1 1
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 Code:1PEB 2.8 42.47 89821 4743 100 0.23341 0.23102 0.2304 0.2792 0.2815 RANDOM 27.576
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] -5.32 -0.9 7.79 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.161 r_dihedral_angle_4_deg 21.575 r_dihedral_angle_3_deg 19.255 r_scangle_it 8.127 r_dihedral_angle_1_deg 5.867 r_scbond_it 5.373 r_mcangle_it 4.994 r_mcbond_it 3.109 r_angle_refined_deg 1.274 r_mcbond_other 1.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.161 r_dihedral_angle_4_deg 21.575 r_dihedral_angle_3_deg 19.255 r_scangle_it 8.127 r_dihedral_angle_1_deg 5.867 r_scbond_it 5.373 r_mcangle_it 4.994 r_mcbond_it 3.109 r_angle_refined_deg 1.274 r_mcbond_other 1.068 r_angle_other_deg 0.94 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28160 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling