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Crystal structure of a putative zinc-binding dehydrogenase (Target PSI-012003) from Sinorhizobium meliloti 1021 bound to NADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 298 Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (MCSG2 #1: 0.2 M Potassium Sodium Tartarate and 20% (w/v) PEG3350 );
Cryoprotection (30% Ethylene glycol); Crystals soaked in 100mM NADP and 100mM
3-hydroxybutyrate-Na
in 15% PEG3350 and 30% ethyleneglycol for at least 30mins, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.56 51.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.62 α = 90 b = 107.62 β = 90 c = 137.741 γ = 90
Symmetry Space Group I 4 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 CCD RAYONIX MX225HE MIRRORS 2011-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-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 2.09 50 99.3 0.118 22.2 13.5 24190 35
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 2.1 2.14 91.5 0.917 2.08 7.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 2.09 50 24190 24174 1229 98.8 0.186 0.185 0.1945 0.22 0.228 RANDOM 41.99
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] -0.11 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 21.781 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 6.349 r_angle_refined_deg 1.546 r_angle_other_deg 0.937 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_4_deg 21.781 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 6.349 r_angle_refined_deg 1.546 r_angle_other_deg 0.937 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2486 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling