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The crystal structure of FAD and ThDP dependent Cyclohexane-1,2-dione Hydrolase (Cdh) from Azoarcus sp. strain 22Lin
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 60% MPD, 0.02M sodium acetate, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.41
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 ADSC QUANTUM 4 2003-12-09 M SINGLE WAVELENGTH 2 1 x-ray M MAD 3 1 x-ray M SINGLE WAVELENGTH 4 1 x-ray M SINGLE WAVELENGTH 1,2,3,4 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4 2 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0052, 1.0093, 1.023 ESRF ID14-4 3 SYNCHROTRON ESRF BEAMLINE ID14-4 1.005 ESRF ID14-4 4 SYNCHROTRON ESRF BEAMLINE ID14-4 1.072 ESRF ID14-4
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 1,2,3,4 1.2 40 77 0.063 12 2.48 259345
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) 1,2,3,4 1.2 1.3 14 0.115 5.1 1.1 20256
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD, MIRAS THROUGHOUT 1.26 5 259345 259345 13524 93.24 0.09782 0.09782 0.09669 0.11963 0.1445 RANDOM 8.189
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] -0.04 -0.04 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.987 r_dihedral_angle_4_deg 15.226 r_dihedral_angle_3_deg 13.543 r_dihedral_angle_1_deg 6.733 r_sphericity_free 5.033 r_sphericity_bonded 4.494 r_scangle_it 3.907 r_scbond_it 3.086 r_mcangle_it 2.356 r_angle_refined_deg 2.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.987 r_dihedral_angle_4_deg 15.226 r_dihedral_angle_3_deg 13.543 r_dihedral_angle_1_deg 6.733 r_sphericity_free 5.033 r_sphericity_bonded 4.494 r_scangle_it 3.907 r_scbond_it 3.086 r_mcangle_it 2.356 r_angle_refined_deg 2.014 r_mcbond_it 1.977 r_rigid_bond_restr 1.849 r_angle_other_deg 1.419 r_mcbond_other 1.228 r_symmetry_vdw_refined 0.402 r_symmetry_vdw_other 0.359 r_symmetry_hbond_refined 0.258 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.21 r_nbd_other 0.198 r_nbtor_refined 0.179 r_chiral_restr 0.125 r_nbtor_other 0.09 r_bond_other_d 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8886 Nucleic Acid Atoms Solvent Atoms 1212 Heterogen Atoms 183
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing