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Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate (compound 3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CPL PDB entry 2CPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
Crystal Properties Matthews coefficient Solvent content 2.73 54.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.494 α = 90 b = 52.406 β = 90 c = 89.337 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2010-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.976 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 34 99.7 0.072 20.34 5 32716 10.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 0.122
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 2CPL 1.5 34 1.38 32589 1995 99.71 0.1535 0.1524 0.153 0.1713 0.1719 13.56
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.1275 f_angle_d 1.1057 f_chiral_restr 0.0705 f_bond_d 0.0097 f_plane_restr 0.0067
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1277 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DENZO data reduction SCALEPACK data scaling PHASER phasing