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Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 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 and 10 mM glycolic acid were mixed with 0.2 ul of the MCSG-I condition #45 (0.2 M Sodium Chloride, 0.1 M Tris:HCl pH 8.5, 25% (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 at 289 K.
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.663 α = 90 b = 65.663 β = 90 c = 151.458 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 100 CCD ADSC QUANTUM 315r 2014-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97912 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 1.4 50 94.8 0.067 0.067 0.072 0.025 10.3 6.8 62557 -3 13.8
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 1.4 1.42 89 0.914 0.986 0.361 0.777 2.1 6.4 2891
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 3KBO 1.4 50 59503 3104 94.87 0.1507 0.1493 0.1488 0.1775 0.1766 RANDOM 20.534
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] 0.4 0.4 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_4_deg 15.329 r_dihedral_angle_3_deg 11.633 r_dihedral_angle_1_deg 5.414 r_angle_refined_deg 1.748 r_mcangle_it 1.106 r_angle_other_deg 1.07 r_mcbond_it 0.699 r_mcbond_other 0.699 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.159 r_dihedral_angle_4_deg 15.329 r_dihedral_angle_3_deg 11.633 r_dihedral_angle_1_deg 5.414 r_angle_refined_deg 1.748 r_mcangle_it 1.106 r_angle_other_deg 1.07 r_mcbond_it 0.699 r_mcbond_other 0.699 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2473 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 55
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing MOLREP phasing HKL-3000 data scaling Coot model building REFMAC refinement PDB_EXTRACT data extraction