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Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus marisnigri JR1 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 277 NANODROP, 30.0% PEG 400, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.34 α = 90 b = 136.71 β = 90 c = 168.12 γ = 90
Symmetry Space Group I 2 2 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 325 mm CCD Flat mirror (vertical focusing) 2007-12-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.97941, 0.91837, 0.97874 SSRL BL11-1
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 1.6 29.386 93.1 0.035 14.07 182268 -3 19.237
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) 1.6 1.66 71.5 0.413 1.9
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 MAD THROUGHOUT 1.6 29.386 182268 9156 93.77 0.229 0.228 0.233 0.259 0.2622 RANDOM 16.446
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] -0.19 0.26 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.464 r_dihedral_angle_4_deg 14.495 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 7.33 r_scangle_it 6.537 r_scbond_it 4.742 r_mcangle_it 2.775 r_mcbond_it 2.193 r_angle_refined_deg 1.765 r_angle_other_deg 1.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.464 r_dihedral_angle_4_deg 14.495 r_dihedral_angle_3_deg 13.033 r_dihedral_angle_1_deg 7.33 r_scangle_it 6.537 r_scbond_it 4.742 r_mcangle_it 2.775 r_mcbond_it 2.193 r_angle_refined_deg 1.765 r_angle_other_deg 1.711 r_mcbond_other 0.756 r_chiral_restr 0.094 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8496 Nucleic Acid Atoms Solvent Atoms 1423 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing autoSHARP phasing