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Anbu (ancestral beta-subunit) from Yersinia bercovieri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NYG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.9 291 0.1M BIS-TRIS PROPANE/HCL
(pH 6.9); 18% w/v PEG 3350; 7.5% v/v ETHYLENE GLYCOL; 0.2M NA2SO4
Crystal Properties Matthews coefficient Solvent content 3.36 63.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.535 α = 90 b = 285.371 β = 91.78 c = 179.213 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 2009-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97935 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.5 50 98.9 0.092 0.087 14.63 5.78 325849
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.57 95.1 1.078 0.98 2.06 5.69
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 5NYG 2.501 49.185 1.36 325791 1983 99.02 0.1831 0.1828 0.1887 0.2298 0.2305 THIN RESOLUTION SHELLS
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 12.735 f_angle_d 1.253 f_chiral_restr 0.054 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 50963 Nucleic Acid Atoms Solvent Atoms 1790 Heterogen Atoms 147
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing Coot model building ARP/wARP model building