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C-terminal domain of RibD from Brucella abortus (5-amino-6-ribosylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate reductase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 294 12% (w/v) PEG 8000 + 0.1 M MES pH 6,2 + 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.34 47.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.91 α = 95.988 b = 56.7 β = 91.249 c = 79.6 γ = 113.164
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 CONVEX PREFOCUSSING MIRROR AND A KIRKPATRICK-BAEZ PAIR OF FOCUSSING MIRRORS 2017-11-26 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) R Merge I (Observed) Rrim I (All) 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 1.92 50.36 98.1 0.085 0.089 0.026 0.999 12.1 11.8 65607 46.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.97 96.9 2.624 2.738 0.779 0.528 1 12.2
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 2B3Z 1.92 50.36 0.57 65607 3274 97.97 0.2361 0.2341 0.2392 0.2741 0.2788 56.94
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 14.6133 f_angle_d 1.6442 f_chiral_restr 0.082 f_bond_d 0.0143 f_plane_restr 0.0111
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6326 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 60
Software Software Software Name Purpose MxCuBE data collection XDS data reduction Aimless data scaling BALBES phasing PHENIX refinement REFMAC refinement Coot model building ARP/wARP model building