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Crystal structure of the Malonyl-ACP Decarboxylase MadB from Pseudomonas putida
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 25% PEG 1500,
0.1 M SPG buffer at pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.88 34.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.739 α = 90 b = 58.282 β = 95.427 c = 57.131 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2021-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.044 56.875 93.9 0.042 0.018 1 16 6.3 101763
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.044 1.107 53.8 0.755 0.46 0.626 1.3 3.4
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE AlphaFold 1.044 56.875 101763 5034 84.965 0.124 0.1223 0.1512 0.1517 15.701
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] 0.153 -0.003 0.129 -0.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.626 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 11.242 r_rigid_bond_restr 7.94 r_dihedral_angle_1_deg 6.651 r_scbond_it 6.229 r_scbond_other 6.226 r_scangle_it 4.829 r_lrange_it 4.829 r_scangle_other 4.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.626 r_dihedral_angle_4_deg 17.367 r_dihedral_angle_3_deg 11.242 r_rigid_bond_restr 7.94 r_dihedral_angle_1_deg 6.651 r_scbond_it 6.229 r_scbond_other 6.226 r_scangle_it 4.829 r_lrange_it 4.829 r_scangle_other 4.82 r_lrange_other 4.595 r_mcangle_it 2.663 r_mcangle_other 2.662 r_mcbond_it 2.592 r_mcbond_other 2.589 r_angle_refined_deg 2.008 r_angle_other_deg 1.619 r_xyhbond_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.251 r_nbd_other 0.249 r_nbd_refined 0.23 r_symmetry_nbd_other 0.187 r_symmetry_nbd_refined 0.184 r_symmetry_xyhbond_nbd_other 0.182 r_nbtor_refined 0.179 r_ncsr_local_group_1 0.149 r_chiral_restr 0.128 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2376 Nucleic Acid Atoms Solvent Atoms 391 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing