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Crystal structure of the D10-P3/IQN17 complex: a D-peptide inhibitor of HIV-1 entry bound to the GP41 coiled-coil pocket
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CZQ PDB entry 1CZQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 10% ETHANOL, 1.5 M SODIUM CHLORIDE, pH 7.5, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 3.51 64.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.702 α = 90 b = 50.702 β = 90 c = 67.858 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 100 CCD ADSC QUANTUM 2000-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.979 NSLS X4A
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 1.5 35 97.2 0.048 16.8 6.5 16309 -3 21.6
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) 1 1.5 1.55 86.8 0.235 4.5 6.1
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 entry 1CZQ 1.5 10 16309 1639 97.2 0.231 0.231 0.2321 0.258 0.2563 RANDOM 28.3
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] 4.6 0.561 -13.44
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 15.7 c_scangle_it 2.68 c_scbond_it 1.85 c_mcangle_it 1.5 c_angle_deg 1.31 c_improper_angle_d 1 c_mcbond_it 0.96 c_bond_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 509 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 1
Software Software Software Name Purpose AMoRE phasing CNS refinement ADSC data collection DENZO data reduction SCALEPACK data scaling