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X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK4 PDB entry 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 2.07 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.9 α = 90 b = 109.3 β = 99.7 c = 67.7 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 IMAGE PLATE MARRESEARCH 1997-05-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 1.0 SSRL BL9-1
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 1.9 67 94 0.054 0.054 21.1 5.9 39417 37052 -3 -3 34.2
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) 1.9 1.93 82 0.352 0.352 3 3.1 1782
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 (All) 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 1AK4 1.9 67.42 -3 39417 37052 3894 94 0.17005 0.17 0.16334 0.1727 0.2324 0.2407 RANDOM 24.56
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] -0.16 -0.24 0.37 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.59 r_dihedral_angle_1_deg 5.758 r_scangle_it 5.125 r_mcangle_it 4.317 r_scbond_it 3.461 r_mcbond_it 3.006 r_angle_refined_deg 2.922 r_angle_other_deg 2.134 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.59 r_dihedral_angle_1_deg 5.758 r_scangle_it 5.125 r_mcangle_it 4.317 r_scbond_it 3.461 r_mcbond_it 3.006 r_angle_refined_deg 2.922 r_angle_other_deg 2.134 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.205 r_chiral_restr 0.196 r_xyhbond_nbd_refined 0.19 r_nbd_other 0.144 r_symmetry_vdw_other 0.137 r_symmetry_vdw_refined 0.113 r_xyhbond_nbd_other 0.032 r_gen_planes_refined 0.019 r_bond_refined_d 0.018 r_gen_planes_other 0.015 r_nbtor_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4779 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building REFMAC refinement X-PLOR phasing