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Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XCV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 300 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP were mixed with 0.2 ul of the MCSG Suite 2 condition #71 (0.2M Na tartrate, 20%w/v PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml TEV solution
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.692 α = 90 b = 65.692 β = 90 c = 151.406 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 300 CCD ADSC QUANTUM 315r 2014-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.979 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.45 50 97.5 0.063 0.063 0.072 0.035 10.9 4 58208 -3 15.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 99.5 0.547 0.633 0.313 0.759 1.9 3.9 2905
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 4xcv 1.45 50 55340 2857 97.57 0.1398 0.1385 0.1381 0.1654 0.1649 RANDOM 19.704
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] 0.02 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.187 r_dihedral_angle_4_deg 15.658 r_dihedral_angle_3_deg 11.446 r_sphericity_bonded 9.285 r_dihedral_angle_1_deg 5.539 r_rigid_bond_restr 2.954 r_mcangle_it 2.221 r_mcbond_it 1.759 r_mcbond_other 1.759 r_angle_refined_deg 1.441
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.187 r_dihedral_angle_4_deg 15.658 r_dihedral_angle_3_deg 11.446 r_sphericity_bonded 9.285 r_dihedral_angle_1_deg 5.539 r_rigid_bond_restr 2.954 r_mcangle_it 2.221 r_mcbond_it 1.759 r_mcbond_other 1.759 r_angle_refined_deg 1.441 r_angle_other_deg 0.943 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2476 Nucleic Acid Atoms Solvent Atoms 487 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement HKL-3000 phasing Coot model building MOLREP phasing HKL-3000 data scaling HKL-3000 data reduction HKL-3000 data collection