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Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Desulfovibrio vulgaris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CUK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 0.2 ul of 19 mg/ml protein in 50 mM Tris pH 7.5, 300 mM NaCl, and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG II condition #21 (1M Ammonium Sulfate, 0.1M Bis-Tris, 1%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 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours
Crystal Properties Matthews coefficient Solvent content 2.58 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.109 α = 90 b = 117.107 β = 90 c = 135.84 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 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) 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 2.5 50.01 99.9 0.091 0.091 8.5 5.2 25228 -3 57.1
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 2.5 2.54 100 0.77 0.666 2.53 5.2 1269
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 2CUK 2.51 50 23947 1240 99.69 0.1768 0.1739 0.1751 0.2298 0.2258 RANDOM 68.79
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] 0.74 1.35 -2.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.794 r_dihedral_angle_4_deg 16.675 r_dihedral_angle_3_deg 12.738 r_dihedral_angle_1_deg 6.109 r_mcangle_it 2.766 r_mcbond_it 1.747 r_mcbond_other 1.747 r_angle_refined_deg 1.362 r_angle_other_deg 0.944 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.794 r_dihedral_angle_4_deg 16.675 r_dihedral_angle_3_deg 12.738 r_dihedral_angle_1_deg 6.109 r_mcangle_it 2.766 r_mcbond_it 1.747 r_mcbond_other 1.747 r_angle_refined_deg 1.362 r_angle_other_deg 0.944 r_chiral_restr 0.074 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 4743 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 24
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling BALBES phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling