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Crystal structure of Tartrate dehydrogenase from Pseudomonas putida complexed with NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FLK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1.65 M ammonium sulfate, 0.2 M ammonium tartrate, 0.01 M DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4 69.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.906 α = 90 b = 182.906 β = 90 c = 66.98 γ = 120
Symmetry Space Group P 6 2 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 IMAGE PLATE MAR scanner 300 mm plate 2008-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.03 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 50 84.7 14251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 80.5 3.3
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 3FLK 2.95 50 11632 604 85 0.26191 0.26017 0.2594 0.29684 0.3056 RANDOM 55.794
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] -0.13 -0.06 -0.13 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.201 r_dihedral_angle_3_deg 21.116 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_1_deg 6.561 r_angle_refined_deg 1.383 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.201 r_dihedral_angle_3_deg 21.116 r_dihedral_angle_4_deg 17.004 r_dihedral_angle_1_deg 6.561 r_angle_refined_deg 1.383 r_nbtor_refined 0.321 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2813 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 45
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling