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Crystal Structure of the Thermostable NADH4-bound old yellow enzyme from Thermoanaerobacter pseudethanolicus E39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 298 50mM Magnesium formate, pH 7.0, vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.38 α = 90 b = 98.556 β = 92.4 c = 95.134 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 315r 2008-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.97 ESRF ID14-4
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 1.501 97.59 91.8 0.065 0.065 10.6 2.7 229398
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) 1.5 1.58 57.9 0.395 0.395 1.9 1.3 20931
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 31.69 139844 7379 98.82 0.157 0.15654 0.1539 0.19397 0.1936 RANDOM 15.302
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 r_dihedral_angle_2_deg 38.042 r_dihedral_angle_4_deg 13.527 r_dihedral_angle_3_deg 12.46 r_dihedral_angle_1_deg 5.467 r_scangle_it 3.524 r_scbond_it 2.19 r_angle_refined_deg 1.313 r_mcangle_it 1.263 r_mcbond_it 0.902 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.042 r_dihedral_angle_4_deg 13.527 r_dihedral_angle_3_deg 12.46 r_dihedral_angle_1_deg 5.467 r_scangle_it 3.524 r_scbond_it 2.19 r_angle_refined_deg 1.313 r_mcangle_it 1.263 r_mcbond_it 0.902 r_nbtor_refined 0.306 r_nbd_refined 0.194 r_symmetry_hbond_refined 0.16 r_symmetry_vdw_refined 0.141 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 10511 Nucleic Acid Atoms Solvent Atoms 1690 Heterogen Atoms 277
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction