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Crystal Structure of Ectodomain of BST-2/Tetherin/CD317 (C2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 298 Crystals were grown at 25C using the microbatch under-oil method by mixing
protein with crystallization buffer containing 100 mM HEPES, pH 7.5, 30% PEG 4000. 3-6% DMSO and 0.2-0.5 mM TCEP were used as additives for optimal crystal growth., EVAPORATION, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.12 42.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 181.65 α = 90 b = 28.59 β = 111.43 c = 94.51 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 110 CCD ADSC QUANTUM 315r 2009-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0717 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 3.2 30 93.8 0.081 0.081 12.5 3 7240 -3
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) 3.2 3.31 96.7 0.569 0.123 1.9
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 3MQ7 3.2 20 6505 338 87.04 0.25832 0.25534 0.2572 0.31526 0.3179 RANDOM 59.349
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] -4.41 -2.23 6.66 -3.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.239 r_dihedral_angle_3_deg 22 r_dihedral_angle_4_deg 17.492 r_scangle_it 15.386 r_scbond_it 8.711 r_dihedral_angle_1_deg 5.625 r_mcangle_it 5.542 r_angle_other_deg 4.219 r_mcbond_it 2.705 r_angle_refined_deg 1.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.239 r_dihedral_angle_3_deg 22 r_dihedral_angle_4_deg 17.492 r_scangle_it 15.386 r_scbond_it 8.711 r_dihedral_angle_1_deg 5.625 r_mcangle_it 5.542 r_angle_other_deg 4.219 r_mcbond_it 2.705 r_angle_refined_deg 1.111 r_chiral_restr 0.062 r_bond_refined_d 0.012 r_gen_planes_refined 0.003 r_gen_planes_other 0.003 r_bond_other_d 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3305 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling