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Crystal structure of amino acid-binding ACT: D-isomer specific 2-hydroxyacid dehydrogenase catalytic domain from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 28 mg/mL protein in 25 mM Hepes pH 7, 0.3 M NaCl, 10% glycerol against Cryo Full condition B3: 50% PEG 400, 5% PEG 1000, 10% glycerol, 0.1 M MES pH 6.0, crystal tracking ID 204157b3, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.91 57.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.891 α = 90 b = 97.891 β = 90 c = 189.215 γ = 120
Symmetry Space Group P 62 2 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 RIGAKU SATURN 944+ 2009-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.15 38.683 97.5 0.09 33.2 17.3 29302
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 82 0.554 3.28 7.7 2412
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 2p9c 2.15 38.683 29249 1485 97.52 0.184 0.182 0.1826 0.216 0.2174 RANDOM 33.332
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] 0.61 0.31 0.61 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.747 r_dihedral_angle_4_deg 14.715 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_1_deg 5.6 r_scangle_it 3.561 r_scbond_it 2.161 r_angle_refined_deg 1.385 r_mcangle_it 1.247 r_mcbond_it 0.676 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.747 r_dihedral_angle_4_deg 14.715 r_dihedral_angle_3_deg 13.216 r_dihedral_angle_1_deg 5.6 r_scangle_it 3.561 r_scbond_it 2.161 r_angle_refined_deg 1.385 r_mcangle_it 1.247 r_mcbond_it 0.676 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3028 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling