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Crystal Structure of Peptidylprolyl Isomerase from Naegleria fowleri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R9H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 NafoA.18272.a.B1.PS38284 at 22.7 mg/ml was mixed 1:1 with Morpheus (h11): 12.5% (w/v) PEG-1000, 12.5% (w/v) PEG-3350, 12.5% (v/v) MPD, 0.1 M bicine/ Trizma base, pH = 8.5, 0.02 M each sodium L-glutmate, DL-alanine, glycine, DL-lysine/ HCl, DL-serine. Tray: 292677h11, puck: pfe9-9.
Crystal Properties Matthews coefficient Solvent content 1.83 32.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.25 α = 90 b = 61.15 β = 90.28 c = 45.76 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 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2017-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.55 45.759 97.6 0.053 0.061 0.997 16.32 4.246 29144 -3 17.06
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 97.2 0.214 0.245 0.975 5.45 4.203
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 1R9H 1.55 45.759 1.39 29135 2024 97.6 0.1569 0.1547 0.1561 0.1867 0.1877 24.657
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 14.146 f_angle_d 0.742 f_chiral_restr 0.053 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1764 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing