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Crystal structure of the WlbA (WbpB) Dehydrogenase from Thermus thermophilus in complex with NAD and UDP-GlcNAcA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O9Z PDB ENTRY 3O9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 15-20% PEG-5000, 100 mM MOPS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.89 57.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.097 α = 90 b = 68.32 β = 94.51 c = 164.122 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 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 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 2 50 91.9 0.073 0.073 62.7 9.1 98909
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) 2 2.03 85.5 0.178 0.127 17.8 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3O9Z 2 30 98901 98901 4966 91.8 0.192 0.189 0.248 0.2558 RANDOM 35.97
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] 3.41 0.06 -0.86 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.086 r_dihedral_angle_4_deg 21.384 r_dihedral_angle_3_deg 18.082 r_dihedral_angle_1_deg 6.876 r_scangle_it 5.361 r_scbond_it 3.345 r_angle_refined_deg 2.478 r_mcangle_it 2.201 r_mcbond_it 1.315 r_chiral_restr 0.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.086 r_dihedral_angle_4_deg 21.384 r_dihedral_angle_3_deg 18.082 r_dihedral_angle_1_deg 6.876 r_scangle_it 5.361 r_scbond_it 3.345 r_angle_refined_deg 2.478 r_mcangle_it 2.201 r_mcbond_it 1.315 r_chiral_restr 0.152 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 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 9781 Nucleic Acid Atoms Solvent Atoms 442 Heterogen Atoms 340
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling