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Crystal structure of FumaraseC from Mannheimia succiniciproducens in complex with Fumarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 20% polyethylene glycol 3350, 0.2M Potassium fluoride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.089 α = 90 b = 104.276 β = 94.1 c = 125.333 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 CCD ADSC QUANTUM 270 2019-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 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) 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 2.1 50 97.9 0.122 0.134 0.055 11.1 4.8 83884
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 96.3 0.273 0.313 0.15 0.846 3.8
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 1YFE 2.12 32.57 79682 4190 96.88 0.1874 0.1846 0.1937 0.241 0.2477 RANDOM 20.324
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] 2.06 -0.73 -0.99 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 16.803 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 1.698 r_angle_other_deg 1.362 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.2 r_dihedral_angle_4_deg 16.803 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_1_deg 7.18 r_angle_refined_deg 1.698 r_angle_other_deg 1.362 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13978 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing