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Crystal structure of the periplasmic domain of XcpY, tI crystal form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.3 M KBr or 0.2 M MgCl2, 0.1 M sodium cacodylate, pH=6.5, gamma-PGA
Crystal Properties Matthews coefficient Solvent content 6.23 80.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.439 α = 90 b = 100.439 β = 90 c = 98.848 γ = 90
Symmetry Space Group I 41 2 2
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 EIGER X 9M 2015-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.5 41 99.7 0.13 16.56 12.97 9039
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.65 98.5 12.02
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5N7S 2.501 40.894 1.35 9018 902 99.61 0.2031 0.2012 0.2048 0.2204 0.2248 random 75.5813
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 2.159 f_angle_d 0.805 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 569 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 19
Software Software Software Name Purpose PHENIX model building PHENIX refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing XDS data scaling