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Crystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH, oxalate and metal ion
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.75 M ammonium sulfate, 0.2 M potassium acetate, 0.02 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.05 59.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.278 α = 90 b = 117.278 β = 90 c = 291.324 γ = 90
Symmetry Space Group P 43 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 IMAGE PLATE MAR scanner 300 mm plate 2008-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9794 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 109.11 99 0.112 21.4 12.2 126431
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 90 0.307 4.97 6.5
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 SAD THROUGHOUT 2 50 126431 6868 99.02 0.20862 0.20764 0.2096 0.22692 0.2284 RANDOM 21.388
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] 0.19 0.19 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.824 r_dihedral_angle_4_deg 15.48 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_1_deg 5.124 r_scangle_it 1.498 r_angle_refined_deg 1.025 r_scbond_it 0.971 r_mcangle_it 0.681 r_mcbond_it 0.459 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.824 r_dihedral_angle_4_deg 15.48 r_dihedral_angle_3_deg 13.481 r_dihedral_angle_1_deg 5.124 r_scangle_it 1.498 r_angle_refined_deg 1.025 r_scbond_it 0.971 r_mcangle_it 0.681 r_mcbond_it 0.459 r_nbtor_refined 0.299 r_nbd_refined 0.178 r_symmetry_vdw_refined 0.123 r_xyhbond_nbd_refined 0.086 r_symmetry_hbond_refined 0.084 r_chiral_restr 0.076 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11248 Nucleic Acid Atoms Solvent Atoms 919 Heterogen Atoms 302
Software Software Software Name Purpose HKL-2000 data collection SHARP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling