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Complex of a chimeric alpha/beta-peptide based on the gp41 CHR domain bound to gp41-5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O3X PDB entry 3O3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 0.2 M MgCl2, 0.1 M Tris pH 8.5, 30% w/v PEG 4000
, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.846 α = 90 b = 56.968 β = 90 c = 103.466 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD 2009-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 50 99.7 0.108 15.6 6.2 16963
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 3O3X 2.1 25 16063 859 99.48 0.17264 0.17057 0.1687 0.21206 0.2059 RANDOM 25.903
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] 1.17 -0.45 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.314 r_dihedral_angle_4_deg 18.706 r_dihedral_angle_3_deg 15.198 r_scangle_it 7.533 r_dihedral_angle_1_deg 5.116 r_scbond_it 4.646 r_mcangle_it 3.035 r_mcbond_it 1.676 r_angle_refined_deg 1.306 r_angle_other_deg 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.314 r_dihedral_angle_4_deg 18.706 r_dihedral_angle_3_deg 15.198 r_scangle_it 7.533 r_dihedral_angle_1_deg 5.116 r_scbond_it 4.646 r_mcangle_it 3.035 r_mcbond_it 1.676 r_angle_refined_deg 1.306 r_angle_other_deg 0.956 r_mcbond_other 0.506 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1857 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 34
Software Software Software Name Purpose MD2 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling