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Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-15-oxa-3,9,12,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (compound 28)
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 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 2.79 55.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.895 α = 90 b = 54.264 β = 90 c = 87.428 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 2012-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.976 ALS 5.0.2
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 34.04 99.9 0.047 35.26 4.7 33123 15.49
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 0.439
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 34.04 1.36 33064 2000 99.64 0.1617 0.1607 0.1616 0.1775 0.1786 18.02
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 9.4004 f_angle_d 1.135 f_chiral_restr 0.0759 f_bond_d 0.0104 f_plane_restr 0.0078
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1259 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing