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Crystal structure of MeaC (Mesaconyl-CoA hydratase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4E3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20%(w/v) PEG3350, 0.2M DL-Malic acid (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.12 42.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.224 α = 90 b = 79.224 β = 90 c = 91.008 γ = 120
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 ADSC QUANTUM 270 2019-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.95 50 98.5 0.108 0.115 0.039 0.998 7.8 6.9 23337
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 1.95 1.98 85.4 0.209 2.2
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 4E3E 1.95 32.12 22150 1180 98.5 0.21341 0.20983 0.216 0.27811 0.2803 RANDOM 32.885
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] -0.46 -0.23 -0.46 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.831 r_dihedral_angle_4_deg 19.73 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 8.041 r_long_range_B_refined 6.023 r_long_range_B_other 6.022 r_scangle_other 4.243 r_mcangle_it 4.004 r_mcangle_other 4.004 r_mcbond_it 2.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.831 r_dihedral_angle_4_deg 19.73 r_dihedral_angle_3_deg 15.153 r_dihedral_angle_1_deg 8.041 r_long_range_B_refined 6.023 r_long_range_B_other 6.022 r_scangle_other 4.243 r_mcangle_it 4.004 r_mcangle_other 4.004 r_mcbond_it 2.935 r_mcbond_other 2.916 r_scbond_other 2.846 r_scbond_it 2.845 r_angle_refined_deg 1.698 r_angle_other_deg 1.268 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 2718 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement HKL-2000 data reduction MOLREP phasing