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Structure of Acetone Carboxylase purified from Xanthobacter autotrophicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 300 mM Calcium acetate, 30% (w/v) PEG3350
Crystal Properties Matthews coefficient Solvent content 2.45 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.915 α = 65.89 b = 139.733 β = 86.54 c = 165.827 γ = 88.69
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92821 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.87 126.06 97.8 0.114 0.984 7 3.5 1990913
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 96.8 0.887 0.528 1.2 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5SVC 1.87 126.06 544134 27977 97.34 0.19291 0.19169 0.2007 0.21694 0.2238 RANDOM 20.5
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] -0.25 0.08 0.17 -0.2 -0.29 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_1_deg 6.144 r_long_range_B_refined 3.951 r_long_range_B_other 3.947 r_scangle_other 1.622 r_angle_refined_deg 1.588 r_mcangle_it 1.027 r_mcangle_other 1.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.589 r_dihedral_angle_4_deg 18.554 r_dihedral_angle_3_deg 13.768 r_dihedral_angle_1_deg 6.144 r_long_range_B_refined 3.951 r_long_range_B_other 3.947 r_scangle_other 1.622 r_angle_refined_deg 1.588 r_mcangle_it 1.027 r_mcangle_other 1.027 r_angle_other_deg 1.01 r_scbond_it 0.992 r_scbond_other 0.992 r_mcbond_it 0.61 r_mcbond_other 0.61 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 51312 Nucleic Acid Atoms Solvent Atoms 4511 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data scaling PHASER phasing