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Crystal structure of PPEP-1(W103F)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A0P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 4 microl 12 mg per ml rPPEP-1 W103F in 20 mM Tris pH 8.5, 200 mM NaCl was mixed with 1 microl precipitant solution containing: 100 mM Tris pH 8.5, 2.1 M ammonium phosphate dibasic. Reservoir volume: 200 microl
Crystal Properties Matthews coefficient Solvent content 1.9 35.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.579 α = 90 b = 66.161 β = 90 c = 118.399 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 80 PIXEL DECTRIS PILATUS 2M-F 2016-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.48 44.12 99.54 14.14 8.5 56407
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.533 0.819 0.836
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 5A0P 1.48 44.117 1.44 56382 1971 99.54 0.1663 0.1651 0.1638 0.1989 0.1999
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 13.942 f_angle_d 0.719 f_chiral_restr 0.059 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3012 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing