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Crystal structure of human 3-hydroxyacyl-thioester dehydratase 2 (HTD2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IQ6 PDB ENTRY 1IQ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 0.5% jeff2001; 1.1M Na(malonate); 0.1M HEPES pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.88 α = 90 b = 99.88 β = 90 c = 77.72 γ = 120
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 2009-08-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97930 Diamond I04
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 1.99 43.25 99.4 0.071 0.071 10.8 3.6 29964
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.1 98.8 0.501 0.501 2.3 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1IQ6 1.99 43.25 28437 28437 1520 99.3 0.17161 0.16992 0.1814 0.20287 0.2115 RANDOM 26.953
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] -1.05 -0.53 -1.05 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.758 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_4_deg 7.705 r_scangle_it 6.392 r_scbond_it 5.464 r_dihedral_angle_1_deg 5.296 r_mcangle_it 4.147 r_mcbond_it 3.27 r_mcbond_other 1.575 r_angle_refined_deg 1.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.758 r_dihedral_angle_3_deg 12.552 r_dihedral_angle_4_deg 7.705 r_scangle_it 6.392 r_scbond_it 5.464 r_dihedral_angle_1_deg 5.296 r_mcangle_it 4.147 r_mcbond_it 3.27 r_mcbond_other 1.575 r_angle_refined_deg 1.452 r_angle_other_deg 1.072 r_chiral_restr 0.087 r_bond_refined_d 0.018 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1840 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 7
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling