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X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M,G89A 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 = 38.467 α = 89.98 b = 111.118 β = 101.6 c = 67.91 γ = 89.9
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 2001-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.97 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 1.7 20 97 0.053 0.053 15.8 2.22 121277 117639 -3 -3 28.1
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) 1.7 1.73 95 0.357 0.357 2.3 2 5780
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.7 19.69 -3 105810 11826 97.12 0.17174 0.1717 0.16537 0.1748 0.23002 0.2375 RANDOM 21.342
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] -0.89 0.04 -0.17 1.57 -0.08 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.126 r_dihedral_angle_1_deg 5.359 r_scangle_it 4.07 r_mcangle_it 3.509 r_scbond_it 2.688 r_angle_refined_deg 2.449 r_mcbond_it 2.328 r_angle_other_deg 1.009 r_symmetry_hbond_refined 0.27 r_symmetry_vdw_refined 0.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.126 r_dihedral_angle_1_deg 5.359 r_scangle_it 4.07 r_mcangle_it 3.509 r_scbond_it 2.688 r_angle_refined_deg 2.449 r_mcbond_it 2.328 r_angle_other_deg 1.009 r_symmetry_hbond_refined 0.27 r_symmetry_vdw_refined 0.269 r_symmetry_vdw_other 0.264 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.215 r_nbd_other 0.207 r_xyhbond_nbd_other 0.15 r_chiral_restr 0.146 r_bond_refined_d 0.019 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9476 Nucleic Acid Atoms Solvent Atoms 1496 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling X-PLOR model building REFMAC refinement X-PLOR phasing