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Crystal structure of a gluconate 5-dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP and tartrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytic MCSG1 screen, E10: 20% (w/V) PEG 3350, 200mM Ammonium tartrate: BuceA.00010.x.B1.PW37241 at 20.44mg/ml + 4mM NADP: cryo: 20% EG + 10mM NADP in 2 steps: tray 285582 e10, puck bdg3-9
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.38 α = 90 b = 91.68 β = 90 c = 121.44 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 100 CCD RAYONIX MX-300 2016-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.65 50 99.3 0.073 0.999 17.93 5.14 116982 -3 12.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 92.4 0.58 0.713 2.14 3.68
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 4ibo 1.65 50 1.35 116823 1965 99.32 0.136 0.1355 0.1352 0.1639 0.1612 14.9941
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 13.05 f_angle_d 0.971 f_chiral_restr 0.065 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7763 Nucleic Acid Atoms Solvent Atoms 1160 Heterogen Atoms 312
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MoRDa phasing XDS data reduction Coot model building PHENIX refinement PDB_EXTRACT data extraction