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X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M Complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK4 PDB ID 1AK4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.08 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.508 α = 90 b = 110.941 β = 101.41 c = 67.932 γ = 90
Symmetry Space Group P 1 21 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 4 2000-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.73 20 96 0.057 0.057 15.9 2.4 58422 56085 -3 -3 31.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.73 1.78 93 0.366 0.366 15.9 2.4 4548
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 ID 1AK4 1.73 19.69 -3 58422 50245 5627 96.03 0.17177 0.16654 0.1775 0.21965 0.2284 RANDOM 23.478
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] -0.86 -0.1 1.45 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.405 r_dihedral_angle_1_deg 5.766 r_scangle_it 4.789 r_mcangle_it 3.804 r_scbond_it 3.146 r_angle_refined_deg 2.794 r_mcbond_it 2.598 r_angle_other_deg 1.668 r_symmetry_hbond_refined 0.244 r_symmetry_vdw_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.405 r_dihedral_angle_1_deg 5.766 r_scangle_it 4.789 r_mcangle_it 3.804 r_scbond_it 3.146 r_angle_refined_deg 2.794 r_mcbond_it 2.598 r_angle_other_deg 1.668 r_symmetry_hbond_refined 0.244 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.217 r_symmetry_vdw_other 0.213 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.18 r_nbd_other 0.16 r_xyhbond_nbd_other 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.016 r_gen_planes_other 0.013 r_bond_other_d 0.001 r_nbtor_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4708 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building REFMAC refinement X-PLOR phasing