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Structural Studies of Acetoacetate Decarboxylase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.95 281 40mM Phosphate buffer pH 5.95, 100mM Sarcosine, 15% PEG 3350, 18% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties Matthews coefficient Solvent content 2.73 54.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.07 α = 90 b = 104.07 β = 90 c = 578.094 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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.0000 NSLS X25
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 2.4 50 98.3 0.093 13 47172
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) 2.4 2.51 93.8 0.354 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.4 45.79 41399 4638 97.6 0.20064 0.19581 0.1934 0.24429 0.243 RANDOM 36.031
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] -0.03 -0.02 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.03 r_dihedral_angle_4_deg 18.908 r_dihedral_angle_3_deg 18.641 r_dihedral_angle_1_deg 6.731 r_scangle_it 1.926 r_angle_refined_deg 1.283 r_scbond_it 1.14 r_mcangle_it 0.711 r_mcbond_it 0.41 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.03 r_dihedral_angle_4_deg 18.908 r_dihedral_angle_3_deg 18.641 r_dihedral_angle_1_deg 6.731 r_scangle_it 1.926 r_angle_refined_deg 1.283 r_scbond_it 1.14 r_mcangle_it 0.711 r_mcbond_it 0.41 r_nbtor_refined 0.307 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.174 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7770 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms
Software Software Software Name Purpose PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing REFMAC refinement