☰ Navigation Tabs
Crystal structure of L-methionine decarboxylase from Streptomyces sp.590 in complexed with 3-methlythiopropylamine (geminal diamine 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 2.15 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.639 α = 90 b = 147.813 β = 99.47 c = 54.187 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 EIGER X 16M 2019-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 1.8 50 98.1 0.068 0.084 0.996 8.3 2.6 88135
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 1.8 1.91 95.9 0.419 0.519 0.87 2 2.4
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 (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 1.8 19.96 85096 4496 99.6 0.20444 0.2027 0.2113 0.23798 0.2455 RANDOM 35.918
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_4_deg 13.495 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 6.118 r_long_range_B_other 6.117 r_scangle_other 3.945 r_mcangle_it 3.554 r_mcangle_other 3.554 r_scbond_it 2.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_3_deg 14.587 r_dihedral_angle_4_deg 13.495 r_dihedral_angle_1_deg 6.557 r_long_range_B_refined 6.118 r_long_range_B_other 6.117 r_scangle_other 3.945 r_mcangle_it 3.554 r_mcangle_other 3.554 r_scbond_it 2.419 r_scbond_other 2.419 r_mcbond_it 2.173 r_mcbond_other 2.17 r_angle_refined_deg 1.46 r_angle_other_deg 1.009 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 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 8160 Nucleic Acid Atoms Solvent Atoms 271 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing