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Crystal structure of the WlbA (WbpB) dehydrogenase from Thermus thermophilus in complex with NAD and alpha-ketoglutarate at 1.45 angstrom resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 15-20% PEG-5000, 100 mM MOPS, 20 mM alpha-ketoglutarate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.87 57.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.781 α = 90 b = 68.199 β = 94.66 c = 164.053 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 210r mirrors 2009-11-14 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97918,0.97953,0.97150 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.449 50 96.8 0.061 0.061 44.4 3.6 270515 270515
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) 1.449 1.48 88.7 0.167 0.167 4.2 2.3 12317
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.449 30 270490 270490 13628 96.7 0.1953 0.1953 0.19367 0.1866 0.22649 0.2153 RANDOM 25.016
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] 1.7 0.3 -0.58 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.505 r_dihedral_angle_4_deg 20.726 r_dihedral_angle_3_deg 15.225 r_dihedral_angle_1_deg 7.308 r_scangle_it 5.751 r_scbond_it 3.725 r_mcangle_it 2.524 r_angle_refined_deg 2.348 r_mcbond_it 1.772 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.505 r_dihedral_angle_4_deg 20.726 r_dihedral_angle_3_deg 15.225 r_dihedral_angle_1_deg 7.308 r_scangle_it 5.751 r_scbond_it 3.725 r_mcangle_it 2.524 r_angle_refined_deg 2.348 r_mcbond_it 1.772 r_chiral_restr 0.141 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9799 Nucleic Acid Atoms Solvent Atoms 1216 Heterogen Atoms 232
Software Software Software Name Purpose HKL-3000 data collection SOLVE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling