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Structure of a UbiA homolog from Archaeoglobus fulgidus bound to Cd2+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 298 30% PEG 550 MME, 100 mM MES, 100 mM CdCl2, 5 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 3.04 59.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.938 α = 90 b = 89.871 β = 90 c = 341.23 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 315 2013-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97920 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 3.067 42.336 98.9 0.043 0.068 0.037 15.8 3.2 15560 15560 106.22
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.067 3.23 99.3 0.643 0.643 0.446 1.1 3.3 2224
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 THROUGHOUT 4TQ5 3.0678 42.336 1.36 15519 772 98.34 0.2669 0.2651 0.273 0.301 0.3096 Random 100.8228
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 13.01 f_angle_d 1.474 f_chiral_restr 0.06 f_plane_restr 0.01 f_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4048 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction PHENIX refinement