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Crystal Structure of 2-hydroxyacyl CoA lyase (HACL) from Rhodospirillales bacterium URHD0017
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 25% (w/v) SOKALAN PA 25 CL, 0.1 M HEPES, pH 7, 0.1 M sodium chloride. ADDITIVE: 0.002 M thiamine diphosphate, 0.02 M CoA-SH, 0.002 M magnesium chloride, 0.002 M ADP
Crystal Properties Matthews coefficient Solvent content 2.59 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.94 α = 90 b = 64.431 β = 90.88 c = 182.693 γ = 90
Symmetry Space Group I 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2019-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.95 52.93 76.4 0.219 0.267 0.151 0.958 3.635 2.96 67457 10.8
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 1.95 2.036 31.25 0.752 0.97 0.604 0.453 2.31
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5dx6 1.95 45.47 1.35 67424 3563 76.22 0.1872 0.1858 0.1864 0.212 0.2132 14.1313
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.627 f_angle_d 0.627 f_chiral_restr 0.044 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8095 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 182
Software Software Software Name Purpose PDB_EXTRACT data extraction PHENIX refinement ARP/wARP model building PHASER phasing Aimless data scaling DIALS data reduction xia2 data reduction JBluIce-EPICS data collection