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Crystal structure of a Short chain dehydrogenase from Burkholderia cenocepacia J2315 in complex with NADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V2G PDB entry 3v2g via Balbes
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 290 Molecular Dimensions Morpheus screen G2: 10% w/v PEG 8000, 20% v/v ethylene glycol: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium L-tartrate, sodium oxamate: 100mM MES/imidazole pH 6.5: BuceA.00010.g.B1.PW37236 at 20.78mg/ml + 4mM NADP: cryo: direct: tray 285571g2, puck yrq2-3
Crystal Properties Matthews coefficient Solvent content 2.35 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.97 α = 90 b = 72.37 β = 100.88 c = 100.53 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN 944+ 2016-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.55 43.945 98 0.047 1 38.65 14.301 137073 -3 10.88
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 1.55 1.59 90.4 0.39 0.911 6.01 8.309 12623
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 PDB entry 3v2g via Balbes 1.55 43.945 1.34 137043 2019 98.04 0.1373 0.1369 0.1363 0.1632 0.1626 15.5888
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 12.951 f_angle_d 1.017 f_chiral_restr 0.064 f_bond_d 0.008 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6919 Nucleic Acid Atoms Solvent Atoms 1314 Heterogen Atoms 244
Software Software Software Name Purpose XDS data reduction XSCALE data scaling MOLREP phasing PHENIX model building Coot model building PHENIX refinement PDB_EXTRACT data extraction