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Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum with partially occupied NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NBV PDB entry 4NBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 21.18 mg/mL BuphA.00010.x.B1.PS37816 + 4 mM NADP + MORPHEUS G2 (269916g2) (10% w/v PEG8000, 20% v/v ethylene glycol, 100 mM MES imidazole, pH 6.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium-L-tartrate, 20 mM sodium oxamate), direct cryoprotection, puck xut9-1
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.9 α = 90 b = 131.9 β = 90 c = 66.51 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 MARMOSAIC 300 mm CCD 2016-03-16 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) 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 1.3 50 100 0.103 0.108 0.997 13.71 9.635 143395 9.25
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 1.3 1.33 100 0.565 0.602 0.881 3.69 8.395
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4NBV 1.3 50 1.34 143315 1996 99.96 0.1434 0.1433 0.152 0.1596 16.2702
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3704 Nucleic Acid Atoms Solvent Atoms 661 Heterogen Atoms 85
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building