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Crystal structure of the two-domain cyclophilinA from Anabaena sp.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RFY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200mM ammonium citrate
20% PEG 3350
10% Morpheus additive screen
Crystal Properties Matthews coefficient Solvent content 2.06 40.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.12 α = 90 b = 103.06 β = 114.74 c = 44.17 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 PIXEL DECTRIS PILATUS 6M 2018-09-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.14 37.38 94.99 0.2 0.2 0.04 0.993 8.1 19.8 115078 14.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.18 91.14 1.8 1 1 0.98 0.4
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 3rfy 1.14 37.38 1.92 115074 11031 94.68 0.1801 0.1791 0.1792 0.1981 0.1982 29.12
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 14.3678 f_angle_d 1.1036 f_chiral_restr 0.0796 f_plane_restr 0.0077 f_bond_d 0.0071
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2608 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DIALS data reduction XSCALE data scaling PHASER phasing