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A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 278 100 mM MES pH 7.0 and Na-citrate ranging from 1.0 to 1.2 M , VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.58 65.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.816 α = 90 b = 99.816 β = 90 c = 126.513 γ = 90
Symmetry Space Group P 41 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 298 2007-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.97854 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 20 93 0.16 5.1 42694 39705 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.15 96.5 0.38 3 4.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.1 20 35980 1891 99.57 0.23241 0.22999 0.27868 0.2471 RANDOM 21.452
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] -0.16 -0.16 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.491 r_dihedral_angle_3_deg 12.885 r_dihedral_angle_4_deg 8.851 r_dihedral_angle_1_deg 4.196 r_angle_refined_deg 1.071 r_scangle_it 0.557 r_scbond_it 0.335 r_mcangle_it 0.319 r_nbtor_refined 0.288 r_mcbond_it 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.491 r_dihedral_angle_3_deg 12.885 r_dihedral_angle_4_deg 8.851 r_dihedral_angle_1_deg 4.196 r_angle_refined_deg 1.071 r_scangle_it 0.557 r_scbond_it 0.335 r_mcangle_it 0.319 r_nbtor_refined 0.288 r_mcbond_it 0.182 r_nbd_refined 0.152 r_chiral_restr 0.064 r_symmetry_hbond_refined 0.063 r_xyhbond_nbd_refined 0.041 r_symmetry_vdw_refined 0.038 r_bond_refined_d 0.009 r_gen_planes_refined 0.002 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 3093 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling Auto-Rickshaw phasing