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Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2
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 7.5 289 0.2 UL OF 11 MG/ML PROTEIN IN 20 MM
HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 0.1% SODIUM AZIDE,
0.5 MM TCEP and 10 mM NADH WERE MIXED WITH 0.2 UL OF THE TOP96 CONDITION #34
(0.2M MAGNESIUM CHLORIDE, 6-HYDRATE, 0.1M HEPES, 25%W/V PEG 3350
PH=7.5) AND EQUILIBRATED AGAINST 1.5 M NACL SOLUTION IN 96 WELL
3 DROP CRYSTALLIZATION PLATE (SWISSCI). BEFORE CRYSTALLIZATION
PROTEIN WAS INCUBATED WITH 1/50 V/V OF 1 MG/ML TEV SOLUTION AT
289 K FOR 1 HOUR
Crystal Properties Matthews coefficient Solvent content 1.95 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.762 α = 90 b = 63.714 β = 90 c = 154.967 γ = 90
Symmetry Space Group C 2 2 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 300 mm CCD Beryllium Lenses 2014-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.978 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.9 50 95.2 0.069 0.073 0.023 21.738 9 22335
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 1.9 1.93 96.9 0.835 0.881 0.276 0.786 2.6 9.6 1110
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 1.9 50 22262 1098 95.2 0.1655 0.1632 0.1732 0.2086 0.2155 RANDOM 39.663
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] -0.82 -1.24 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.127 r_dihedral_angle_4_deg 16.421 r_dihedral_angle_3_deg 13.682 r_dihedral_angle_1_deg 5.555 r_mcangle_it 2.154 r_angle_refined_deg 1.639 r_mcbond_it 1.518 r_mcbond_other 1.518 r_angle_other_deg 0.837 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.127 r_dihedral_angle_4_deg 16.421 r_dihedral_angle_3_deg 13.682 r_dihedral_angle_1_deg 5.555 r_mcangle_it 2.154 r_angle_refined_deg 1.639 r_mcbond_it 1.518 r_mcbond_other 1.518 r_angle_other_deg 0.837 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2270 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose BLU-MAX data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing HKL-3000 phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction