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Crystal structure of Pyrococcus abyssi Pbp11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 200 mM potassium thioycyanate, 25% PEG 3350.
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.581 α = 90 b = 54.156 β = 95.058 c = 62.551 γ = 90
Symmetry Space Group I 1 2 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-F 2017-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.64 42.42 99.2 0.076 0.038 0.998 10.4 5.6 21583 21.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.73 97.3 0.792 0.404 0.848 2.4 5.5
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 1XE1 1.64 42.42 1.36 21519 1075 98.81 0.1949 0.1935 0.1944 0.2222 0.2261 32.33
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 13.8703 f_angle_d 1.2157 f_chiral_restr 0.0825 f_bond_d 0.0116 f_plane_restr 0.0076
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1344 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 54
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling PHASER phasing