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Crystal structure of the complex between GP41 fragment N36 and fusion inhibitor C34/S138A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AIK PDB ENTRY 1AIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 293 100MM SODIUM ACETATE BUFFER, PH4.0, 400MM MAGNESIUM CHLORIDE, 12% ETHANOL, pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.09 α = 90 b = 49.09 β = 90 c = 56.4 γ = 120
Symmetry Space Group P 3 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 113 IMAGE PLATE RIGAKU RAXIS VII 2008-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 33.95 99.7 0.061 19.1 10.13 4248
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 100 0.406 4.3 9.63
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 1AIK 2.2 18.52 4037 195 99.8 0.215 0.212 0.208 0.283 0.2793 RANDOM 40.69
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.86 r_dihedral_angle_4_deg 30.046 r_dihedral_angle_3_deg 19.225 r_dihedral_angle_1_deg 6.326 r_scangle_it 6.062 r_scbond_it 3.751 r_mcangle_it 2.243 r_angle_refined_deg 2.06 r_mcbond_it 1.379 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.86 r_dihedral_angle_4_deg 30.046 r_dihedral_angle_3_deg 19.225 r_dihedral_angle_1_deg 6.326 r_scangle_it 6.062 r_scbond_it 3.751 r_mcangle_it 2.243 r_angle_refined_deg 2.06 r_mcbond_it 1.379 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.295 r_symmetry_hbond_refined 0.261 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.128 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 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 593 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling