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Crystal structure of an SDR from Burkholderia ambifaria in complex with NADPH with a TCEP adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 MCSG1 G4 (291317g4): 100mM Potassium tartrate, 20% PEG3350, 8mM NADP, protein conc. 20.8mg/mL, cryo 20% ethylene glycol: puck ID opk4-15
Crystal Properties Matthews coefficient Solvent content 2.22 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.09 α = 90 b = 64.09 β = 90 c = 119.17 γ = 90
Symmetry Space Group P 42 21 2
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 315r 2017-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.000 ALS 8.2.1
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 1.45 50 100 0.051 1 30 10.158 44832 -3 12.93
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 1.45 1.49 100 0.574 0.619 0.863 3.44 7.15
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 5idx 1.45 34 1.34 44828 1998 100 0.149 0.148 0.1487 0.164 0.1648 17.93
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 18.786 f_angle_d 1.146 f_chiral_restr 0.081 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1872 Nucleic Acid Atoms Solvent Atoms 358 Heterogen Atoms 72
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling Coot model building PDB_EXTRACT data extraction XDS data reduction MOLREP phasing