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Crystal structure of the HIV-2 neutralizing Fab fragment 7C8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 293 50 mM ammonium sulphate, 25% (w/v) PEG 8000 and 2.5% (v/v) PEG 400, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.97 58.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.071 α = 90 b = 100.071 β = 90 c = 196.763 γ = 120
Symmetry Space Group P 32 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 MAR CCD 130 mm 2003-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
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 2.7 44.6 100 0.07 0.07 21.1 7.7 32045
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1I9J 2.7 42.8 30420 30420 1615 99.8 0.229 0.226 0.273 0.2738 RANDOM 88.34
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] 4.39 2.19 4.39 -6.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.132 r_dihedral_angle_4_deg 17.975 r_dihedral_angle_3_deg 16.43 r_dihedral_angle_1_deg 5.806 r_angle_refined_deg 1.065 r_scangle_it 1.05 r_scbond_it 0.608 r_mcangle_it 0.536 r_mcbond_it 0.285 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.132 r_dihedral_angle_4_deg 17.975 r_dihedral_angle_3_deg 16.43 r_dihedral_angle_1_deg 5.806 r_angle_refined_deg 1.065 r_scangle_it 1.05 r_scbond_it 0.608 r_mcangle_it 0.536 r_mcbond_it 0.285 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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 6677 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 6
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling