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Crystal structure of Slr0204, a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase from Synechocystis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 298 1.35 M NaH2PO4/0.8 M K2HPO4, 400 mM Li2SO4, 100 mM CAPS, pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.496 α = 90 b = 54.496 β = 90 c = 191.093 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2009-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.9 37.8 100 0.129 17.4 7.7 23811 23811
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 1.9 1.95 100 0.99 2.2 7.9
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 (All) 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 2HX5 1.9 35.92 23704 23704 1169 99.88 0.17164 0.17164 0.17011 0.1807 0.20074 0.2111 RANDOM 28.174
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] 0.24 0.24 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.113 r_dihedral_angle_3_deg 14.17 r_dihedral_angle_4_deg 11.666 r_dihedral_angle_1_deg 7.849 r_angle_refined_deg 0.927 r_angle_other_deg 0.604 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.113 r_dihedral_angle_3_deg 14.17 r_dihedral_angle_4_deg 11.666 r_dihedral_angle_1_deg 7.849 r_angle_refined_deg 0.927 r_angle_other_deg 0.604 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2156 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 4
Software Software Software Name Purpose ADSC data collection PHENIX model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing