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Crystal structure of L-methionine decarboxylase from Streptomyces sp.590 in complexed with 3-methlythiopropylamine (external aldimine form).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M MMT buffer pH 6.0, 23.5 % (w/v) PEG1500
Crystal Properties Matthews coefficient Solvent content 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.176 α = 90 b = 147.495 β = 99.79 c = 54.065 γ = 90
Symmetry Space Group C 1 2 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 PILATUS 2M-F 2019-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.00000 Photon Factory AR-NE3A
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 1.61 50 98.2 0.09 0.113 0.993 6.9 2.6 122379
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 1.61 1.71 97.4 0.733 0.914 0.63 1.3 2.6
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 7CIF 1.61 19.92 118163 6098 99.82 0.1771 0.17578 0.1883 0.20287 0.212 RANDOM 25.482
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_4_deg 16.778 r_dihedral_angle_3_deg 13.944 r_dihedral_angle_1_deg 6.003 r_long_range_B_refined 5.502 r_long_range_B_other 5.5 r_scangle_other 3.902 r_mcangle_it 3.103 r_mcangle_other 3.102 r_scbond_it 2.396
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.36 r_dihedral_angle_4_deg 16.778 r_dihedral_angle_3_deg 13.944 r_dihedral_angle_1_deg 6.003 r_long_range_B_refined 5.502 r_long_range_B_other 5.5 r_scangle_other 3.902 r_mcangle_it 3.103 r_mcangle_other 3.102 r_scbond_it 2.396 r_scbond_other 2.396 r_mcbond_it 1.881 r_mcbond_other 1.881 r_angle_refined_deg 1.526 r_angle_other_deg 1.012 r_chiral_restr 0.118 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 8150 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing