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Crystal structure of a putative NAD(P) dependent gluconate 5-dehydrogenase from Beutenbergia cavernae(EFI target EFI-502044) with bound NADP (low occupancy)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O03 PDB ENTRY 3o03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffuction 4.6 298 Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (100 mM NaAcetate pH 4.6, 2 M NaFormate); Cryoprotection (Reservoir + 20% glycerol), sitting drop vapor diffuction, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.47 α = 90 b = 115.47 β = 90 c = 76.182 γ = 90
Symmetry Space Group P 43 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 MIRRORS 2011-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9793 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2 81.685 99.9 0.071 20.1 10.9 35340 35340
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 99.9 0.424 0.424 1.8 10.5 5048
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3o03 2 42.745 34249 34249 1712 96.8 0.1633 0.1633 0.1616 0.161 0.1946 0.1943 RANDOM 36.6866
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] -1.3279 -1.3279 2.6559
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.725 f_angle_d 1.034 f_chiral_restr 0.095 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3556 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 96
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction CBASS data collection MOSFLM data reduction PHENIX phasing