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Crystal structure of NADPH-dependent 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH and oxalate
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 5.5 289 0.2 ul of 14.8 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG Suite 1 condition #93 (0.1M Bis-Tris, 25%w/v PEG 3350 pH=5.5) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/13 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours
Crystal Properties Matthews coefficient Solvent content 2.14 42.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.945 α = 90 b = 70.124 β = 90 c = 126.615 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 225 mm CCD Beryllium Lenses 2015-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 50 99.9 0.077 0.077 6.1 6.5 49321 -3 27.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 99.9 0.863 0.748 1.71 6.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4xcv 1.9 50 46819 2311 99.95 0.1566 0.1546 0.1976 0.1917 RANDOM 36.901
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] 0.89 -0.69 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_4_deg 16.591 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_1_deg 5.475 r_mcangle_it 2.886 r_mcbond_it 2.247 r_mcbond_other 2.246 r_angle_refined_deg 1.328 r_angle_other_deg 0.918 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.432 r_dihedral_angle_4_deg 16.591 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_1_deg 5.475 r_mcangle_it 2.886 r_mcbond_it 2.247 r_mcbond_other 2.246 r_angle_refined_deg 1.328 r_angle_other_deg 0.918 r_chiral_restr 0.076 r_bond_refined_d 0.009 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 4882 Nucleic Acid Atoms Solvent Atoms 592 Heterogen Atoms 108
Software Software Software Name Purpose MD2 data collection HKL-3000 phasing HKL-3000 data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling