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Crystal structure of the complex between gp41 fragment N36 and fusion inhibitor SC34EK
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 VAPOR DIFFUSION, HANGING DROP 4 277 100mM Sodium Acetate Buffer, pH4.0, 200mM Ammonium Sulphate, 14% PEG2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.85 74.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.014 α = 90 b = 105.014 β = 90 c = 78.308 γ = 120
Symmetry Space Group P 31 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 RIGAKU JUPITER 210 2007-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1
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 2.1 90 99.7 0.122 29461 35.9
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 PDB ENTRY 1AIK 2.1 19.85 27843 1494 99.76 0.21464 0.21337 0.2106 0.23803 0.2379 RANDOM 29.931
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 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.11 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 15.896 r_dihedral_angle_1_deg 3.788 r_scangle_it 3.725 r_scbond_it 2.203 r_mcangle_it 1.228 r_angle_refined_deg 1.015 r_mcbond_it 0.806 r_nbtor_refined 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.11 r_dihedral_angle_4_deg 18.85 r_dihedral_angle_3_deg 15.896 r_dihedral_angle_1_deg 3.788 r_scangle_it 3.725 r_scbond_it 2.203 r_mcangle_it 1.228 r_angle_refined_deg 1.015 r_mcbond_it 0.806 r_nbtor_refined 0.28 r_nbd_refined 0.183 r_symmetry_hbond_refined 0.158 r_xyhbond_nbd_refined 0.149 r_symmetry_vdw_refined 0.125 r_chiral_restr 0.075 r_bond_refined_d 0.01 r_gen_planes_refined 0.003 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 1806 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing