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HIV-1 Nef protein in complex with engineered Hck-SH3 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EFN PDB entry 1EFN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 285 100 mM Tris buffer, 5% ethylne glycol, 10% PEG 8000, 0.2 M MgCl2, 15 mM MnCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.692 α = 90 b = 65.692 β = 90 c = 279.068 γ = 90
Symmetry Space Group P 41 21 2
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 2009-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 69.77 99.5 18.2 40486 40486 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 99
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1EFN 2 50 40486 40486 2148 99.97 0.16989 0.168 0.1772 0.20544 0.2097 RANDOM 54.995
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] -0.24 -0.24 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.172 r_dihedral_angle_4_deg 15.987 r_dihedral_angle_3_deg 15 r_dihedral_angle_1_deg 7.236 r_scangle_it 5.127 r_scbond_it 3.32 r_mcangle_it 2.472 r_angle_refined_deg 1.823 r_mcbond_it 1.466 r_angle_other_deg 1.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.172 r_dihedral_angle_4_deg 15.987 r_dihedral_angle_3_deg 15 r_dihedral_angle_1_deg 7.236 r_scangle_it 5.127 r_scbond_it 3.32 r_mcangle_it 2.472 r_angle_refined_deg 1.823 r_mcbond_it 1.466 r_angle_other_deg 1.021 r_mcbond_other 0.432 r_chiral_restr 0.139 r_bond_refined_d 0.026 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3046 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing