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The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.18 43.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.6 α = 90 b = 123.6 β = 90 c = 144.3 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 100 CCD MARMOSAIC 225 mm CCD 2005-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00 SLS X10SA
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 1.1 40 84.8 0.068 13.58 6.1 388867 379045 12.26
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 1.1 1.2 49.9 0.487 2.7 3.6 50802
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 known crystal structure THROUGHOUT 1.2 10 333858 333858 16593 97.17 0.15 0.15 0.149 0.1576 0.176 0.1809 RANDOM 12.78
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] 0.75 0.75 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 16.822 r_dihedral_angle_3_deg 13.719 r_sphericity_free 8.377 r_dihedral_angle_1_deg 6.736 r_sphericity_bonded 5.477 r_scangle_it 4.005 r_scbond_it 3.235 r_mcangle_it 2.394 r_rigid_bond_restr 2.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 16.822 r_dihedral_angle_3_deg 13.719 r_sphericity_free 8.377 r_dihedral_angle_1_deg 6.736 r_sphericity_bonded 5.477 r_scangle_it 4.005 r_scbond_it 3.235 r_mcangle_it 2.394 r_rigid_bond_restr 2.139 r_angle_refined_deg 2.052 r_mcbond_it 1.995 r_mcbond_other 1.766 r_angle_other_deg 1.391 r_symmetry_vdw_refined 0.317 r_symmetry_vdw_other 0.309 r_xyhbond_nbd_refined 0.25 r_nbd_refined 0.222 r_symmetry_hbond_refined 0.212 r_nbd_other 0.192 r_nbtor_refined 0.171 r_chiral_restr 0.128 r_nbtor_other 0.084 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8886 Nucleic Acid Atoms Solvent Atoms 1268 Heterogen Atoms 290
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection XDS data reduction