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Crystal Structure of Putative glucose 1-dehydrogenase from Burkholderia cenocepacia in complex with NADP and a potential reaction product
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MOW apo structure 4mow, as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 287 RigakuReagents MCSG1 screen, condition C7: 200mM CaCl2, 100mM TrisBase/HCl pH 8.5, 25% (w/V) PEG 4000: BuceA.00010.f.B1.PW37227 at 19.9mg/ml + 4mM NADP: tray: 274300 C7: cryo: 15% EG + NADP: puck: PWJ4-6.
Crystal Properties Matthews coefficient Solvent content 2.14 42.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.72 α = 90 b = 116.66 β = 90 c = 180.62 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 Beryllium Lenses 2016-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.55 50 99.7 0.091 0.099 0.998 13.54 6.202 257945 17.727
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 99.9 0.46 0.505 0.885 3.53 5.979
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 apo structure 4mow, as per MoRDa 1.55 49.08 1.34 257694 2057 99.7 0.1388 0.1387 0.1388 0.1591 0.1589 0 13.04
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 12.5643 f_angle_d 1.0206 f_chiral_restr 0.0667 f_plane_restr 0.0092 f_bond_d 0.0091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14042 Nucleic Acid Atoms Solvent Atoms 2201 Heterogen Atoms 522
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building