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A structural basis for substrate and stereo selectivity in octopine dehydrogenase (ODH-NADH-Pyruvate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 285 100 mM MES pH 7.0, 1.15 M Na-citrate, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96 α = 90 b = 96 β = 90 c = 117.8 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 100 CCD MAR CCD 165 mm 2007-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 2.5 50 99.9 0.062 26 6.2 17543 17525 2 2
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) 2.6 2.7 99.9 0.36 0.361 5.1 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3C7A 2.5 19.75 16311 859 100 0.25441 0.25348 0.2531 0.27228 0.2715 RANDOM 36.947
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] 0.82 0.82 -1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.382 r_dihedral_angle_3_deg 14.895 r_dihedral_angle_4_deg 12.645 r_dihedral_angle_1_deg 4.951 r_angle_refined_deg 1.035 r_scangle_it 0.599 r_mcangle_it 0.393 r_scbond_it 0.358 r_nbtor_refined 0.296 r_mcbond_it 0.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.382 r_dihedral_angle_3_deg 14.895 r_dihedral_angle_4_deg 12.645 r_dihedral_angle_1_deg 4.951 r_angle_refined_deg 1.035 r_scangle_it 0.599 r_mcangle_it 0.393 r_scbond_it 0.358 r_nbtor_refined 0.296 r_mcbond_it 0.217 r_nbd_refined 0.177 r_symmetry_hbond_refined 0.152 r_symmetry_vdw_refined 0.12 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.065 r_bond_refined_d 0.006 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 2991 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection Integrate data reduction XSCALE data scaling PHASER phasing